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Linking models across scales to assess the viability and restoration potential of a threatened population of steelhead (Oncorhynchus mykiss) in the Middle Fork John Day River, Oregon, USA
Supplementary resource (1)
Data
December 2017
... In a collaborative effort with the Integrated Status and Effectiveness Monitoring Program (ISEMP), a life cycle model (LCM) for steelhead was developed using regional habitat parameters from the Columbia Habitat Monitoring Program (CHaMP) and fish data specific to the MFJDR (McHugh et al. 2017). The modeling framework leveraged CHaMP habitat data to estimate reach-level juvenile rearing and adult spawning capacity as a function of physical habitat. ...
... In a collaborative effort with the Integrated Status and Effectiveness Monitoring Program (ISEMP), a life cycle model (LCM) for steelhead was developed using regional habitat data and fish data specific to the MFJDR (McHugh et al. 2017). Two restoration scenarios were modeled; one scenario aimed to enhance rearing capacity and survival for juveniles by providing cooler summer temperatures and another that aimed to increase the population's juvenile carrying capacity by increasing the structural/hydraulic complexity of select reaches (via large wood and structural additions). ...
... The McHugh et al. (2017) model indicated that restoration designed to reduce temperature was more influential than those designed to increase habitat complexity. 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 reduction. ...
In the Middle Fork John Day River (MFJDR) basin in Oregon, nearly two centuries of land management practices have contributed to the decline of federally threatened Mid-Columbia summer steelhead Oncorhynchus mykiss and non-listed spring Chinook Salmon O. tshawytscha. Beaver trapping, road building, clear-cut logging, fire suppression, channel rerouting, floodplain/wetland drainage, grazing, and mining have all impacted the MFJDR through time. While the most damaging of these practices have been curtailed, their harmful legacies remain, including degraded floodplain function and connectivity, reduced habitat quantity and diversity, increased water temperature, and altered hydrology and sediment routing. These key limiting factors have been identified as negatively impacting steelhead and salmon recovery in the MFJDR (CBMRCD 2005; Carmichael and Taylor 2010). Habitat restoration is a primary strategy to address the limiting factors in Columbia Basin tributaries that hinder salmonid recovery in the Pacific Northwest (PNW), including the MFJDR.
... Numerous habitat factors and management actions affect salmon survival during the freshwater life stages. Habitat restoration showed potential for ameliorating future climate-induced warming of streams in a modeling study of the Grande Ronde (Justice et al. 2017) and John Day Rivers (McHugh et al. 2017). ...
... In a study focused on the Middle Fork John Day River in Oregon, McHugh et al. (2017) leveraged reach-scale habitat models linked to basin-scale life cycle models to evaluate restoration priorities for steelhead O. mykiss. Results suggested that in terms of reducing quasi-extinction risk for steelhead, increasing riparian vegetation to reduce limiting stream temperatures was more beneficial than adding woody debris to increase channel complexity. ...
Impacts of Climate Change on Salmon of the Pacific Northwest
A review of the scientific literature published in 2017
... These challenges often apply more broadly to electrofishing data. They are: (1) sampling sites are rarely randomly located and the effects of management actions are unlikely to be uniformly distributed, so production needs to be estimated within a "model-based" rather than a "designbased" framework (McHugh et al., 2017) (2) capture probability can vary over time, between passes and life-stages (as in this study) and across habitats (3) quantifying habitat at large (> reach) spatial scales necessary for upscaling production estimates can be challenging (4) electrofishing samples collected on river networks are not necessarily independent depending on life-stage and distance between sampling locations (5) fish densities will vary with stock level and may be subject to density-dependent processes. ...
... More recently, production has been estimated by modelling fish counts as a function of GIS-derived habitat covariates (McHugh et al., 2017) and then scaling production near continuously across the river using the spatial distribution of covariates. Similarly, Isaak et al. (2017) estimated fish densities near continuously using a river network model that incorporated spatial covariance to improve inference and predictions, but only considered linear responses between abundance and habitat. ...
There are increasing calls for “conservation stocking” to counter declines in Atlantic salmon (Salmo salar) populations, the assumption being that stocking can bypass population bottlenecks and increase recruitment over natural processes. However, there are too few quantitative studies with sufficient data to assess the efficacy of conservation stocking. The Girnock Burn is a unique long-term monitoring site where adult and juvenile salmon numbers have been monitored for over 50 years, including 11 years with conservation stocking. Adults were monitored at a fixed trap and juveniles were monitored by electrofishing. In stocked years, ova were incubated in surface water to reduce density-independent over-winter mortality. In eight years, eyed ova were stocked at uniform densities to reduce local density-dependence. In three years, stocking replicated natural spatial variability in ova deposition removing any potential benefits of reduced local density-dependence. Juvenile production was estimated by summing the product of reach-scale density estimates and river area obtained from a novel spatial statistical river network model that incorporated the effects of capture probability, habitat and stock level. Capture probability varied with life-stage (age 0+ fry or ≥1+ parr), electrofishing pass and day of the year, but importantly also exhibited a positive temporal trend across years. Survival from ova to fry was density-independent and higher under uniform stocking than natural spawning or simulated natural spawning. Under uniform stocking, fry densities varied smoothly with altitude, while under natural spawning and simulated natural spawning, fry exhibited a more patchy distribution. Increased fry production did not translate to increased parr production, which was strongly density-dependent. This likely reflected the inability of fry to move between stocked locations and suitable overwintering habitat, decreasing survival between fry and parr life-stages. Consequently, there was no overall benefit of stocking. The modelling framework used in this study provides a valuable approach for interpreting long-term datasets where site locations, equipment and staffing vary over time. The long-term Girnock dataset was valuable in separating management action from natural population regulation and permitting understanding of ecological processes. The study indicates that conservation stocking can be ineffective, even where implemented to best scientific standards. It is therefore recommended that a detailed understanding of local population dynamics is obtained, and a realistic appraisal of the expected benefits of stocking is undertaken, before management actions are considered.
... Projections: Four out of the nineteen papers that were considered projections were vulnerability assessments that used a variety of qualitative and quantitative methods [305,[323][324][325]. Six papers focused on inland trout species [32,149,[326][327][328][329], while nine focused on salmon. Quantitative projection models for anadromous species captured Atlantic salmon [330,331], [314,333], steelhead trout [314,334], and most frequently, Chinook salmon [27,314,335,336]. ...
As we confront novel environmental challenges, a full understanding of the physical and biological processes that govern species responses to climate change will help maintain biodiversity and support conservation measures that are more robust to irreducible uncertainty. However, climate impacts are so complex, and the literature on salmon and trout is so vast that researchers and decision makers scramble to make sense of it all. Therefore, we conducted a systematic literature review of climate impacts on salmon and anadromous trout as a resource for stakeholders, managers, and researchers. We reviewed studies published from 2010 to 2021 that address climate impacts on these fish and organized them in a database of 1169 physical and 1853 biological papers. Papers are labeled with keywords across eight categories related to subject matter and study methods. We compared the literature by biological process and life stage and used these comparisons to assess strengths and weaknesses. We then summarized expected phenotypic and genetic responses and management actions by life stage. Overall, we found the largest research gaps related to species interactions, behavioral responses, and effects that carry over across life stages. With this collection of the literature, we can better apply scarce conservation resources, fill knowledge gaps, and make informed decisions that do not ignore uncertainty.
... In addition, coordinated efforts by agencies collecting data that improve accessibility and transparency can contribute to a wealth of data with which to address a wide range of questions. These data repositories can provide the information necessary to parameterize relationships that can facilitate extrapolation across scales (McHugh et al., 2017) and assess management or restoration over time (Harrison et al., 2019). ...
Worldwide, many productive rivers are dam‐regulated and rely on flow management strategies that must balance support of ecological processes with human water use. One component of evaluating this balance is to understand ecological consequences of alternative flow management strategies, which has often been accomplished by coupling population dynamics models with models that relate streamflow to habitat availability and quality. Numerous methods assign habitat availability to locations within a river basin: These include fine‐scale field‐measured values that are extrapolated to other locations within the basin having similar physical characteristics or equation‐driven values created by functions of model‐predicted values of physical characteristics. The array of options for creating habitat models is evolving rapidly as high‐resolution remote‐sensing data becomes more accessible and computational capacity improves. Our objective was to identify trade‐offs among approaches that assign habitat relationships to large rivers and to create a decision support tool to supplement choices of extent and granularity. Using a selection of case studies that represent a breadth of scales and diverse trade‐offs, we demonstrate the need for a transparent process of data evaluation and assessment to determine the appropriate fit for model scope or context that best supports management needs and recognize sources of uncertainty. The structured approach proposed here aims at improving future model development and refine population dynamics models that inform the management of rivers.
... However, revisions to the current BioenergeticHSC program will provide an alternative option to deal with this bias. Users will be able to directly import depth and velocity transect data for different flows, and the software will directly calculate predicted NREI at each transect point for the speci- bypassing the need for HSCs and their associated drawbacks (e.g., Railsback, 2016), and the direct use of NREI as an index of habitat quality to assess flow effects has already been applied using other bioenergetic drift-foraging modeling platforms (e.g., (Hayes et al., 2015;McHugh et al., 2017). ...
Habitat simulation approaches (e.g., PHABSIM) have been used to model instream flows in thousands of streams and rivers and remain the most widely implemented detailed instream flow methodology. However, recent studies suggest that conventional habitat simulation models incorporate assumptions that may systematically underestimate instream flow needs, particularly for drift‐feeding fish. These include: (i) systematic biases in velocity habitat suitability curves (HSCs) caused by territoriality where dominant individuals displace subordinate fish to lower velocity micro‐habitats at high densities, thereby inflating the fitness value of low velocities; (ii) habitat simulation models do not account for flow effects on prey flux to drift‐feeding fishes, which may decrease more rapidly with reduced flow than does available habitat; (iii) use of focal velocities to construct traditional HSCs, which systematically underestimates velocity preference within the broader foraging arena of a drift‐feeding fish, and (iv) inadvertent use of low‐velocity HSCs associated with daytime refuging behavior from predators that may underestimate the higher velocities necessary for crepuscular foraging. Collectively, these factors suggest that current and historic flow prescriptions using traditional habitat simulation methods may underestimate optimal rearing flows for salmonids and other drift‐feeding species by anywhere from 10 to 50%. This implies that traditional instream flow management may be failing to provide the intended level of protection for drift‐feeding fishes in multiple streams at landscape scales. We provide guidelines for identifying contexts where model predictions are likely to be biased and approaches for correcting them.
... Consequently, despite the legal identification of the riparian zone as critical habitat (Pearson 2007), loss of this habitat has continued with limited enforcement (e.g., Hutchings and Post 2013). This is problematic because riparian restoration is essential if listed species like Salish sucker and associated salmonid communities are to persist in agricultural and urbanizing landscapes, particularly under climate change (DeBano et al. 2016;McHugh et al. 2017). Federal SARA legislation in Canada follows a stewardship model (Illical and Harrison 2007), and failure to deal effectively with riparian protection on private land indicates that reliance on voluntary stewardship may fail without a regulatory backstop (Langpap and Wu 2004;Wollstein and Davis 2017). ...
To understand the effects of widespread urbanization and agricultural impacts on recovery of Salish sucker, a federally threatened Catostomid endemic to the lower Fraser Valley of British Columbia, we assessed i) the current extent and effects of hypoxia on the distribution of Salish sucker and juvenile salmonids, ii) potential drivers of hypoxia, and iii) management options for hypoxia mitigation. Over 40% of sucker critical habitat experiences hypoxia (dissolved oxygen (DO) < 4 mg·l-I) by late summer, indicating widespread non-compliance with water quality guidelines. The strong positive relationship between seasonal hypoxia and temperature (R2= 0.53) and negative relationship with streamflow (R2= 0.78) indicates that hypoxia is driven by a synergy between low summer flows, elevated temperatures, and high primary production associated with nutrient enrichment (eutrophication). Sucker show strong selection against high water temperatures and weaker negative selection against low DO; juvenile salmonids show very strong selection against both high temperatures and low DO. Climate projections for declining summer flows and elevated temperatures indicate worsening trends in DO without intensive watershed-scale management to reduce nutrient loads.
... Furthermore, compensatory actions by salmon in later life experiences can mitigate effects of harsh conditions in early life experiences (Al-Chokhachy et al. 2019). Thus, lifecycle analyses that account for these multiple factors and their sequences can more accurately describe the impact of a stressor in the greater context of population-level responses (McHugh et al. 2017). One approach that ecologists may use to develop reference points is to generate ecological indicators and corresponding salmon response surfaces (i.e., expected performance described in multidimensional space) for life stages of lifecycle models. ...
Ecology is often governed by nonlinear dynamics. Nonlinear ecological relationships can include thresholds-incremental changes in drivers that provoke disproportionately large ecological responses. Among the species that experience nonlinear and threshold dynamics are Pacific salmon (Oncor-hynchus spp.). These culturally, ecologically, and economically significant fishes are in many places declining and management focal points. Often, managers can influence or react to ecological conditions that salmon experience, suggesting that nonlinearities, especially thresholds, may provide opportunities to inform decisions. However, nonlinear dynamics are not always invoked in management decisions involving salmon. Here, we review reported nonlinearities and thresholds in salmon ecology, describe potential applications that scientists and managers could develop to leverage nonlinear dynamics, and offer a path toward decisions that account for ecological nonlinearities and thresholds to improve salmon outcomes. It appears that nonlinear dynamics are not uncommon in salmon ecology and that many management arenas may potentially leverage them to enable more effective or efficient decisions. Indeed, decisions guided by nonlinearities and thresholds may be particularly desirable considering salmon management arenas are often characterized by limited resources and mounting ecological stressors, practical constraints, and conservation challenges. More broadly, many salmon systems are data-rich and there are an extensive range of ecological contexts in which salmon are sensitive to anthropogenic decisions. Approaches developed to leverage nonlinearities in salmon ecology may serve as examples that may inform analogous approaches in other systems and taxa.
... These assessments, however, generally do not explicitly account for numerous other abiotic conditions, such as water temperature, turbidity, and nutrient availability, which can also mediate restoration outcomes (but see Beechie et al., 2012). For example, if water temperatures are outside the thermal optimum for target species, or if ambient nutrient concentrations strongly limit aquatic productivity, then ecological recovery may fall short of expectations defined by geomorphic conditions alone (McHugh et al., 2017;Sanderson et al., 2009). Furthermore, many restoration approaches that seek to ease conditions limiting target fish populations, such as riparian vegetation restoration, nutrient augmentation, and nonnative species removal, cannot be adequately evaluated by geomorphic assessments because these approaches do not directly modify the physical structure of the stream. ...
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 development of bioenergetics-based foraging models for drift-feeding fish gained momentum in the early 1990s (Hughes & Dill 1990;Hill & Grossman 1993) and their use has steadily increased in research and applied contexts since then (e.g. Urabe et al. 2010;Wall et al. 2016;McHugh et al. 2017;. They are appealing because they provide a functional understanding of fish foraging behaviour and habitat selection (Piccolo et al. 2014;Rosenfeld et al. 2014). ...
... One of the primary goals of amending planning documents (e.g., USDA/USDI 1994) in the 1990s was to increase the likelihood that new management practices would maintain the viability of native salmonids (Ratner et al. 1997;McHugh et al. 2017). The primary mechanism for improving stream conditions was to limit resource management such as timber harvest, road construction, livestock grazing, and other activities near streams (Boisjolie et al. 2017;Roper et al. 2018). ...
Historic management actions authorized or allowed by federal land management agencies have had a profound negative effect on salmon, trout, and char populations and their habitats. To rectify past failings, in the 1990s, federal agencies in the Interior Columbia River Basin modified how they conducted land management activities to foster the conservation of aquatic species. The primary policy changes were to provide additional protection and restoration of lands near streams, lakes, and wetlands. What remains uncertain was whether these changes have altered the trajectory of stream habitat conditions. To address this question, we evaluate the status and trends of ten stream habitat attributes; wood frequency, wood volume, residual pool depth, percent pool, pool frequency, pool tail fines (< 6 mm), median particle size, percent undercut banks, bank angle, and streambank stability in managed and reference catchments following changes in management policies. Our review of these data support the hypothesis that changes made in management standards and guidelines in the 1990s are related to improved stream conditions. Determining the precise magnitude of changes in stream conditions that resulted from the modification of land management policies is difficult due to the shifting environmental baseline. By understanding and accounting for how changes in stream conditions reflect improved land management policies and broader environmental trends, federal agencies will be better situated to make project level decisions that benefit aquatic resources.
... Ultimately, practitioners need to weigh the benefits of various HSM approaches with their associated logistical and computational constraints. If fully dynamic predictions of population-level responses to habitat and flow modification are the ultimate objective (Anderson et al., 2006;Lancaster & Downes, 2010), complex mechanistic models offer clear advantages (Ayllón et al., 2016;McHugh et al., 2017;Railsback et al., 2009). However, sufficient information to parameterise and validate these approaches will probably continue to limit their utility in many situations, and their general use in the immediate future. ...
Quantitative habitat suitability models (HSMs) are frequently used to inform the conservation and management of lotic organisms, often in the context of instream flow management. Correlative statistical models relating hydraulic variables to habitat preferences (habitat suitability curves based on use:availability ratios) are the most common form of HSM, but face significant criticism on the grounds that habitat preference may not reflect the fitness consequences of habitat use. Consequently, there has been a drive to develop mechanistic approaches that link habitat to direct correlates of fitness.
Bioenergetic foraging models relating hydraulic conditions to energy balance are particularly well‐developed for drift‐feeding fishes (e.g. salmonids) and show promise as a more mechanistic approach to modelling suitability. However, these models are rarely validated empirically or quantitatively compared with correlative HSMs. We addressed these gaps by comparing the ability of a bioenergetics‐based HSM and two correlative HSMs (a traditional suitability index and a resource selection function) to predict density and growth of stream salmonids (juvenile steelhead, Oncorhynchus mykiss , and coastal cutthroat trout, Oncorhynchus clarki ).
Suitability estimates differed between the approaches, with both correlative models predicting higher suitability relative to the bioenergetic model at shallow depths and low to intermediate velocities, but lower suitability as depth increased. The bioenergetic model explained over 90% of variation in trout growth, compared to c . 50% for the correlative model. The bioenergetic model was also better at predicting fish density; however, the improvement was less striking and a high proportion of variation remained unexplained by either method.
Differences in suitability estimates between approaches probably reflect biotic interactions (e.g. territorial displacement or predation risk) that decouple realised habitat use from energetics‐based estimates of habitat quality. Results highlight fundamental differences between correlative HSMs, based on observed habitat use, and mechanistic HSMs, based on the physiology and behaviour of the focal taxa. They also suggest that mechanistic bioenergetics‐based models provide more rigorous estimates of habitat suitability for drift‐feeding stream fishes. The bioenergetics approach is readily accessible to instream flow practitioners because model predictions are expressed in terms of traditional habitat suitability curves.
... Oncorhynchus mykiss (McHugh et al., 2017). ...
Introduction paper (7.5 credit course) - a part of my licentiate degree at Karlstad University.
... we decomposed the natural origin SAR return estimates into ocean age specific survival (S1, S2, S3) and maturation probabilities (m1, m2, and m3) that could yield an overall SAR and returning adult age structure on par with the observed data (Table 6). While the observed return-at-age pattern is a function of non-identifiable parameters, the approach used here places constraints on survival and maturation probabilities by age that allow parameter estimation (see McHugh et al. 2017 for an example and rationale). Also note that our model assumes a single SAR representative of an 'average' outmigrant experience and makes no attempt to parse transported vs. in -river individuals; thus, the assumption is the data for 1993-2011 brood years are a reasonable average of future mainstem/ocean conditions. ...
The following describes continued progress toward assessment of Chinook salmon populations and habitat restoration opportunities within the upper Grande Ronde River (UGR) and Catherine Creek (CC) watersheds using a life-cycle modeling (LCM) framework. The work presented here extends LCM development efforts previously initiated by the Columbia River Inter-Tribal Fish Commission (CRITFC) and included as part of the Independent Scientific Advisory Board's (ISAB) 2017 review of LCM efforts in the interior Columbia Basin (chapter 9.f in ISAB 2017). Ultimately, these efforts are intended to provide an analytical tool that will guide long-term restoration and recovery strategies for two threatened Chinook Salmon populations under changing climatic conditions.
... could be helpful in terms of building more realistic expectations for defining what is physically and geomorphically possible at a given site. If the Yakama Nation is interested in restoration for recovering salmonid populations, the framework of network-capacity modelling coupled to life-cycle models could be very fruitful ( McHugh et al. 2017). ET-AL would be happy to help the Yakama Nation with applying any of these additional network modes. ...
This report presents an application of the Beaver Restoration Assessment Tool 2.0.0 (BRAT; http://brat.riverscapes.xyz/), a tool for building realistic expectations for partnering with beaver in conservation and restoration (Macfarlane et al. 2017). In this application, we analyzed all the perennial rivers and streams within the Yakama Nation Reservation, which includes portions of the Lower Yakima, and Klickitat watersheds (8-digit USGS Hydrologic Unit Code (HUC 8)). As part of Contract Modification 1, we expanded our analysis to include Rock Creek watershed (10-digit USGS Hydrologic Unit Code (HUC 10)), which is presented in the body of this report. As part of Contract Modification 2 we again expanded our analysis and included the White Salmon, Little White Salmon and Wind River watersheds (HUC 10’s). We present results of Modification 2 separately in Appendix A: BRAT model outputs for Little White Salmon, White Salmon and Wind River watersheds because this request occurred after this report had been written and the modification did not include funding to include this analysis in a report.
... Furthermore, these models potentially represent robust management tools because they can be linked to multidimensional models of stream flow and used to produce more realistic estimates of habitat quality and quantity at reach and watershed scales (Hayes, Goodwin, Shearer, Hay, & Kelly, 2016;McHugh et al., 2017;. ...
Species conservation requires understanding the mechanistic processes of habitat selection and their effects on fitness. Nonetheless, there are few fitness‐based habitat selection models for aquatic organisms. We examined multiple aspects of foraging behaviour of nonanadromous Dolly Varden Charr (Salvelinus malma) in Panguingue Creek, Alaska, USA and applied these data to test a fitness‐based microhabitat selection model. Velocity negatively affected prey capture success, positively affected holding velocity, and had no effect on reactive distance. Dominance was a better predictor of prey capture success than length difference between competitors, but there was no relationship between these variables and holding velocity or reactive distance. We used the velocity–prey capture success relationship to parameterise the microhabitat habitat selection model and compared the predicted optimal holding velocity to the 95% confidence interval (24.9–29.3 cm/s) of holding velocities occupied by Dolly Varden (N = 29) in Panguingue Creek. The prediction of 24.0 cm/s fell just slightly (0.9 cm/s) outside the lower limit of the confidence interval; the model barely failed to predict holding velocity for this species in Panguingue Creek. Although this discrepancy fell within measurement error, model failure also may have been due to influence of high turbulence on fish holding velocities in the creek, low sample sizes imposed by permitting limitations, or field logistical issues. The relationship between velocity and prey capture success is an important aspect of drift feeder habitat selection. Our optimal holding velocity prediction for Dolly Varden should aid in the management and conservation of this species.
... Where nonnative species are not an imminent threat, the USFS promotes aquatic organism passage projects, permitting movements by native species to these cold-water areas. Projects restoring stream channel structure (e.g., narrowing and deepening stream channels) and promoting riparian vegetation to increase shade can moderate the predicted future effects of climate change (McHugh et al. 2017). The agency's management direction to protect aquatic systems can foster the persistence of narrowly distributed endemics, but this task may be more difficult in regions where NFS lands are interspersed among other land ownerships, such as the southeastern United States (Jenkins et al. 2015). ...
The U.S. Department of Agriculture Forest Service (USFS) manages 193 million acres of public lands across 43 states and Puerto Rico. The original intent behind reserving lands managed by the USFS was to improve and protect forests, secure favorable conditions for water flows, and furnish a continuous supply of timber for the nation. Through time national forests have evolved, so they are managed for a broad array of uses. Differing expectations have led to conflicts between aquatic conservation and other aspects of the USFS’ mandate. In the 1990s, these conflicting goals came to a head with the listing of the northern spotted owl Strix occidentalis caurina and the need to better protect streams that fostered populations of anadromous salmonids. To better balance these conflicting uses, the agency placed additional emphasis on conserving and restoring aquatic systems by integrating conservation concepts into the forest planning process. If the USFS is to succeed in protecting and restoring aquatic biodiversity, it must continue to address traditional challenges such as minimizing the effects of timber harvest, roads, grazing, and mining on aquatic systems while improving policies and practices regarding contemporary challenges such as climate change and invasive species. This article is protected by copyright. All rights reserved.
... ). Accordingly, the coupled effect of riparian vegetation restoration on salmon habitat availability and rusty crayfish spread via stream cooling could also be assessed by integrating HexSim with additional models(McHugh et al., 2017;Ruesch et al., 2012).Our sensitivity analysis, together with a review of the literature, provided confidence regarding the model parameter estimates (Supporting Information Appendix S4 and S5). By varying parameters in small (±20%) and large increments (−75%, +100%), we demonstrated that the population size projected by our model was sensitive to changes in juvenile survival and intrinsic fecundity for population size, but was largely invariant to carrying capacity or the number of propagules seeding the initial invasion. ...
Aim
Mounting ecological impacts of invasive species on freshwater ecosystems are among the greatest challenges confronting ecologists and decision‐makers in conserving biodiversity and ecosystem function. Tools to slow the proliferation of aquatic invasive species are still needed to guide the allocation of limited resources more effectively and efficiently once a species is already established. Here we develop mechanistic models to recreate the invasion history of the rusty crayfish Faxonius rusticus in the John Day River (JDR) basin, forecast its future distribution, and evaluate the management efficiency of, and trade‐offs among, population control actions.
Location
John Day River Basin, Oregon.
Methods
The spread and control of rusty crayfish in the JDR was simulated with a spatially explicit individual‐based model (SEIBM) whereby the life history of each crayfish in the population is modelled in response to environmental conditions that vary across space and time. The model was calibrated by comparing modelled rusty crayfish spread throughout the JDR to known occurrences according to three comprehensive surveys.
Results
Our model accurately reproduced historical rusty crayfish distribution data for 2005, 2010, and 2016 with a specificity and sensitivity of ~80%. Leveraging this realistic model of the spread of rusty crayfish, we show that rapid management actions to the initial invasion would have resulted in an opportunity to slow the spread of rusty crayfish. We instead predict that rusty crayfish will reach the mainstem of the Columbia River by 2025, at which our model predicts that the crayfish population will number on the order of 10⁸ individuals over more than 1100 km of river throughout the watershed and progress into critical salmon spawning habitat.
Main conclusion
This study demonstrates that SEIBMs can provide unique insight into the future distribution of aquatic invasive species and concretely support decision‐makers in choosing an optimal control strategy.
... We have successfully generated accurate and precise hydraulic models for more than 2200 field surveys, covering more than 900 unique reaches, producing estimates of depth and velocity fields. These products have been instrumental in the development of high resolution models estimating energetic capacity and habitat suitability for salmonids (Wall et al., 2016;Wheaton et al., 2017;McHugh et al., 2017). ...
... However, these maps are based on predictions of water depth values in the stream and on the landscape for extreme rainfall events [6]. Hydrology and hydraulic models can be useful for predicting these depth values, although, like many other models, these models are only as reliable as the underlying assumptions in the model's structure Hydrology 2018, 5, 9 2 of 10 and parameters [7,8]. The assimilation of water depth measurements, as a post-processing technique, has the potential to reduce the error between model predictions and observations in order to generate more reliable flood inundation maps [9]. ...
This study proposes a framework that (i) uses data assimilation as a post processing technique to increase the accuracy of water depth prediction, (ii) updates streamflow generated by the National Water Model (NWM), and (iii) proposes a scope for updating the initial condition of continental-scale hydrologic models. Predicted flows by the NWM for each stream were converted to the water depth using the Height Above Nearest Drainage (HAND) method. The water level measurements from the Iowa Flood Inundation System (a test bed sensor network in this study) were converted to water depths and then assimilated into the HAND model using the ensemble Kalman filter (EnKF). The results showed that after assimilating the water depth using the EnKF, for a flood event during 2015, the normalized root mean square error was reduced by 0.50 m (51%) for training tributaries. Comparison of the updated modeled water stage values with observations at testing locations showed that the proposed methodology was also effective on the tributaries with no observations. The overall error reduced from 0.89 m to 0.44 m for testing tributaries. The updated depths were then converted to streamflow using rating curves generated by the HAND model. The error between updated flows and observations at United States Geological Survey (USGS) station at Squaw Creek decreased by 35%. For future work, updated streamflows could also be used to dynamically update initial conditions in the continental-scale National Water Model.
... Current and potential or historic habitat condition bound the range of feasible habitat rehabilitation scenarios. The impacts these scenarios have on fish population processes and the resulting long-term effects on the population trajectory can be assessed through various quantitative frameworks ( McHugh et al. 2017). Biological relevance should be determined by science-based fish-habitat relationships with a documented and understandable origin and specific to species, life-stage and season. ...
Many population metrics for wild steelhead Oncorhynchus mykiss are unquantified due to complex early life history strategies and a lack of juvenile age data. Juvenile steelhead can rear in freshwater systems for up to 7 years, with overlapping size distributions among age‐classes. As logistics for sampling and aging fish can be challenging, there are benefits to utilizing age–length keys (ALKs). We examined the potential benefits of applying ALKs to unaged juvenile steelhead from a rotary screw trap and to determine whether stratifying trapping data by season could improve accuracy in assigning ages to unaged fish. Additionally, we examined the effects of reducing samples of aged fish using a uniform sampling design in which there was a fixed number of aged fish across all length intervals of the size distributions. Using a leave‐one‐out cross validation method with aged fish, we found that ALKs assigned unbiased ages to unaged fish. When including fish with assigned ages from ALKs, results of mean length‐at‐age and brood year abundance estimates between using proportional‐sampled aged fish and uniform‐sampled aged fish were comparable. Typically, absolute differences in estimated brood year abundances were improved if age‐assigned fish were included, and mean absolute error did not exceed 0.4 years for any of the methods examined. Although seasons had a significant effect on mean length at age, overall brood year estimates of juvenile abundance derived from stratifying data by season did not notably differ from pooling summer and fall seasons together, likely because there was a higher portion of juveniles emigrating in the fall compared to the summer. Age–length keys can benefit trapping operations and aid in filling data gaps in age‐based movement and survival for steelhead by being able to accurately assign ages to unaged fish and include more data for population analyses.
Historically, anadromous steelhead Oncorhynchus mykiss and spring‐run Chinook Salmon O. tshawytscha used high‐elevation rivers in the Sierra Nevada of California but were extirpated in the 20th century by construction of impassable dams. Plans to reintroduce the fish by opening migratory passage across the dams and reservoirs can only succeed if upstream habitats have the capacity to support viable populations of each species. To estimate capacity in the Tuolumne and Merced rivers of the central Sierra Nevada, we used a high‐resolution approach based on remote sensing and dynamic habitat modeling. Our results suggested that for both species in both systems, sediment grain sizes would support widespread spawning and the water temperatures, depths, and velocities would generate ample capacity for fry and juveniles. However, the unregulated Merced River was consistently too warm for adult Chinook Salmon to hold in the dry season prior to spawning, while the regulated Tuolumne River maintained a cooler, more stable thermal regime with a capacity for thousands of holding adults. In our high‐resolution approach, we also discovered several specific physical controls on life history expression, including thermal constraints on the timing of spawning, hydraulic prompts for downstream migration of fry, divergence of the hydraulic niches of steelhead and Chinook Salmon, and a key but uncertain role for thermal tolerance in adult Chinook Salmon. Our results suggested that steelhead reintroduction could succeed in either system and Chinook Salmon could succeed in the Tuolumne River if passage strategies account for large numbers of migrant fry and juveniles driven downstream by winter storms and snowmelt. The Merced River appeared too warm for adult Chinook Salmon, which raises questions about the current limited understanding of thermal tolerance in holding adults. Our study shows how a high‐resolution approach can provide valuable insights on specific limiting factors that must be addressed for reintroduction to succeed.
Diversity in steelhead Oncorhynchus mykiss (anadromous Rainbow Trout) is often characterized by varying time
spent in freshwater and saltwater environments. However, ontogenetic shifts are not often highlighted as an important
diversity characteristic in salmonids. Larger water bodies can play a key role in population stability by buffering limited
resources in smaller tributary systems. Based on freshwater and saltwater ages of adult steelhead in Fish Creek,
Idaho, there were 12 different life history trajectories observed. Juvenile abundance varied from 12,083 (SE =
1,225.7) to 62,463 (SE = 1,753.8), with ages ranging from young of the year (age 0) to 4 years. Adult abundance fluctuated
from 17 (SE < 0.1) to 499 (SE = 67.1), and total age of adults varied from 3 to 7 years. Diversity was most
evident in juvenile movement and rearing strategies. We observed four types of movement and rearing pathways in
which juveniles either directly migrated to the ocean from Fish Creek or resided for up to three winters in main-stem
river habitat in the Clearwater River basin prior to ocean migration. Most juveniles emigrated in the fall at age 2,
and most ocean-emigrating smolts were age 3. Subsequently, most juveniles resided for at least one additional winter
period before ocean migration. Juvenile diversity was also reflected in adult ages; the mean proportion that spent 3
years in freshwater was 0.55 (SE = 0.03), and the mean proportion that spent 2 years in freshwater was 0.41 (SE =
0.03). Adult sex ratio was female biased (mean ± SE = 0.66 ± 0.02), with a higher proportion of females (0.89 ± 0.03)
than males (0.65 ± 0.05) residing in the ocean for at least 2 years. Density-dependent mechanisms were evident in
juvenile rearing habitat in Fish Creek for cohorts of high female abundance. Population productivity potentials can be
met when tributary and main-stem rearing habitat can be utilized, and this will be essential in attaining recovery
goals.
Habitat Suitability Curves (HSCs) are the biological component of habitat simulation tools used to evaluate instream flow management trade‐offs (e.g., the Physical Habitat Simulation Model). However, traditional HSCs based on empirical observations of habitat use relative to availability have been criticized for generating biased estimates of flow requirements and for being poorly transferable across locations. For fish like salmonids that feed on drifting invertebrates, bioenergetics‐based foraging models that relate habitat conditions to net energy gain offer an alternative approach that addresses some of these shortcomings. To make this technique more accessible for practitioners, we present free and user‐friendly software for generating bioenergetics‐based HSCs. The software also allows sensitivity analyses of HSCs to factors like fish size or prey abundance as well as direct integration of hydraulic data. While some caveats remain, bioenergetic HSCs should offer a more rigorous and credible means for quantifying habitat suitability for instream flow modelling.
The first comprehensive Geomorphic Assessment of the Lower White River, Utah and Colorado, including valley landform delineation, river reach typing, geomorphic condition, 80-year channel change record, results of riparian condition assessment (R-CAT), and case study scenarios of endangered fish and invasive vegetation removal.
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.
KEYWORDS: Salmonid habitat, geomorphic condition, geomorphic recovery, river styles
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 lifecycle. 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.
The removal of wood from river channels was once a common practice in an effort to reduce flooding and improve transport of timber and other products. River restoration practitioners are increasingly adding large wood into rivers to restore natural channel characteristics and aquatic habitat degraded by these past practices. Most restoration projects use wood in a static manner by anchoring trees and rootwads in place. The use of mobile wood additions-a restoration approach where added wood is allowed to migrate naturally through the channel at high flows-is being pioneered on Nash Stream in northern New Hampshire. While both methods are effective, our implementation and subsequent monitoring shows that mobile wood more closely mimics natural recruitment to, and transport and accumulation within, river systems, and provides a cost-effective method of increasing wood densities in hard-to-reach locations or with limited stands of riparian trees.
Spatial variation in fish densities across river networks suggests that the influence of food and habitat resources on assemblages varies greatly throughout watersheds. Conceptual models predict that in situ primary production should vary with river characteristics, but the influence of autochthonous resource availability on the capacity for river reaches to support fish is poorly understood. We estimated primary production throughout the South Fork and Middle Fork of the John Day River, Oregon, by measuring diel cycles in dissolved oxygen (DO) during July 2013. Using these data, we (1) evaluated the extent to which juvenile salmonid abundance and resource limitation correlated with areas of high gross primary production (GPP), (2) developed models to predict GPP from both site-level measurements and remotely sensed data, and (3) made predictions of GPP across the entirety of the Middle Fork John Day River (MFJD) network and assessed the utility of these spatially continuous predictions for describing variation fish densities at broad scales. We produced reliable estimates of GPP at sites where DO loggers were deployed using measurements of solar exposure, water temperature, and conductivity measured at each site, as well as surrogates for these data estimated from remote sensing data sources. Estimates of GPP across fish sampling sites explained, on average, 58–63% of the variation in juvenile salmonid densities during the summer sampling period, and 51–83% during the fall sampling period, while continuous network predictions of GPP explained 44% of the variation in fish densities across 29 km of the MFJD. Further, GPP explained nearly half of the variation in juvenile steelhead dietary resource limitation, as inferred from bioenergetics modeling results. These results comprise a first effort at quantifying variation in autochthonous production across an entire river network and, importantly, provide a much-needed food-web context for guiding more effective fish and habitat management.
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 lifecycle. 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.
Population size estimates for stream fishes are important for conservation and management, but sampling costs limit the extent of most estimates to small portions of river networks that encompass 100s–10 000s of linear kilometres. However, the advent of large fish density data sets, spatial-stream-network (SSN) models that benefit from nonindependence among samples, and national geospatial database frameworks for streams provide the components to create a broadly scalable approach to population estimation. We demonstrate such an approach with density surveys for trout species from 108 sites in a 735 km river network. Universal kriging was used to predict a continuous map of densities among survey locations, and block kriging (BK) was used to summarize discrete map areas and make population estimates at stream, river, and network scales. The SSN models also accommodate covariates, which facilitates hypothesis testing and provides insights about factors affecting patterns of abundance. The SSN–BK population estimator can be applied using free software and geospatial resources to develop valuable information at low cost from many existing fisheries data sets.
Understanding how stream temperature responds to restoration of riparian vegetation and channel morphology in context of future climate change is critical for prioritizing restoration actions and recovering imperiled salmon populations. We used a deterministic water temperature model to investigate potential thermal benefits of riparian reforestation and channel narrowing to Chinook Salmon populations in the Upper Grande Ronde River and Catherine Creek basins in Northeast Oregon, USA. A legacy of intensive land use practices in these basins has significantly reduced streamside vegetation and increased channel width across most of the stream network, resulting in water temperatures that far exceed the optimal range for salmon growth and survival. By combining restoration scenarios with climate change projections, we were able to evaluate whether future climate impacts could be offset by restoration actions. A combination of riparian restoration and channel narrowing was predicted to reduce peak summer water temperatures by 6.5 °C on average in the Upper Grande Ronde River and 3.0 °C in Catherine Creek in the absence of other perturbations. These results translated to increases in Chinook Salmon parr abundance of 590% and 67% respectively. Although projected climate change impacts on water temperature for the 2080s time period were substantial (i.e., median increase of 2.7 °C in the Upper Grande Ronde and 1.5 °C in Catherine Creek), we predicted that basin-wide restoration of riparian vegetation and channel width could offset these impacts, reducing peak summer water temperatures by about 3.5 °C in the Upper Grande Ronde and 1.8 °C in Catherine Creek. These results underscore the potential for riparian and stream channel restoration to mitigate climate change impacts to threatened salmon populations in the Pacific Northwest.
Drift-foraging models offer a mechanistic description of how fish feed in flowing water and the application of drift-foraging bioenergetics models to answer both applied and theoretical questions in aquatic ecology is growing. These models typically include nonlinear descriptions of ecological processes and as a result may be sensitive to how model inputs are summarized because of a mathematical property of nonlinear equations known as Jensen’s inequality. In particular, we show that the way in which continuous size distributions of invertebrate prey are represented within foraging models can lead to biases within the modeling process. We begin by illustrating how different equations common to drift-foraging models are sensitive to invertebrate inputs. We then use two case studies to show how different representations of invertebrate prey can influence predictions of energy intake and lifetime growth. Greater emphasis should be placed on accurate characterizations of invertebrate drift, acknowledging that inferences from drift-foraging models may be influenced by how invertebrate prey are represented.
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.
Contributions of terrestrial-, freshwater-, and marine-derived prey resources to stream fishes vary over time and space, altering the energy pathways that regulate production. In this study, we determined large-scale use of these resources by juvenile Chinook and coho salmon (Oncorhynchus tshawytscha and Oncorhynchus kisutch, respectively) in the glacial Susitna River, Alaska. We resolved spatial and temporal trophic patterns among multiple macrohabitat types along a 97 km segment of the river corridor via stable isotope and stomach content analyses. Juvenile salmon were supported primarily by freshwater-derived resources and
secondarily by marine and terrestrial sources. The relative contribution of marine-derived prey to rearing salmon was greatest in the fall within off-channel macrohabitats, whereas the contributions of terrestrial invertebrate prey were generally greatest during midsummer, across all macrohabitats. No longitudinal (upstream–downstream) diet pattern was discernable. These results highlight large-scale spatial and seasonal patterns of energy flow and the dynamic interplay of pulsed marine and terrestrial prey subsidies to juvenile Chinook and coho salmon in a large, complex, and relatively pristine glacial river.
Hundreds of millions of dollars have been spent on stream restoration projects to benefit salmonids and other aquatic species across the Pacific Northwest, though only a small percentage of these projects are monitored to evaluate effectiveness and far fewer are tracked for more than 1 or 2 years. The Washington State Salmon Recovery Board and the Oregon Watershed Enhancement Board have spent more than US$500 million on salmonid habitat restoration projects since 1999. We used a multiple before-after–control-impact design to programmatically evaluate the reach-scale physical and biological effectiveness of a subset of restoration actions. A total of 65 projects in six project categories (fish passage, instream habitat, riparian planting, livestock exclusion, floodplain enhancement, and habitat protection) were monitored over an 8-year period. We conducted habitat, fish, and macroinvertebrate surveys to calculate the following indicators: longitudinal pool cross section and depth, riparian shade and cover, large woody debris volumes, fish density, macroinvertebrate indices, and upland vegetation condition class. Results indicate that four categories (instream habitat, livestock exclusions, floodplain enhancements, and riparian plantings) have shown significant improvements in physical habitat after 5 years. Abundance of juvenile Coho Salmon Oncorhynchus kisutch increased significantly at fish passage projects and floodplain enhancement projects, but significant results were not detected for other fish species. Moreover, the biological response indicators of juvenile salmonid abundance and macroinvertebrate indices showed declines at instream habitat and habitat protection projects, respectively. Our results indicate that a subset of projects can be effectively evaluated programmatically, but power and sample size estimates indicate that two or more years of preproject data are necessary to adequately determine the effectiveness of many project types, particularly for fish. Programmatic evaluations of project effectiveness should include adequate preproject sampling and multiseason monitoring for fish species to address issues of variability that are likely to be encountered in large-scale monitoring programs.Received September 16, 2015; accepted February 7, 2016
Two approaches to ecological restoration planning, limiting-factors analysis and process-based restoration, are employed in efforts to recover endangered salmonid species throughout the Pacific Northwest of North America. Limiting-factors analysis seeks to identify physical limitations to fish production that may be addressed by habitat restoration; it is known as the "Field of Dreams" hypothesis (i.e., if you build it, they will come). Process-based restoration, in contrast, assumes that protection and/or restoration of watershed-scale processes will best achieve self-sustaining habitat features that support salmon populations. Two case studies from the Columbia River basin (northwestern USA) display current efforts to integrate these two restoration approaches to improve salmonid populations. Although these examples both identify site-specific habitat features to construct, they also recognize the importance of supporting key watershed processes to achieve restoration goals. The challenge in advancing the practice of restoration planning is not in simply acknowledging the conceptual benefits of process-based restoration while maintaining a traditional focus on enumerating site-specific conditions and identifying habitat-construction projects, but rather in following process-based guidance during recovery planning and, ultimately, through implementation of on-the-ground actions. We encourage a realignment of the restoration community to truly embrace a process-based, multi-scalar view of the riverine landscape.
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 means of assessing the efficacy of watershed-scale restoration.
Substantial research effort has been devoted to understanding stream-dwelling salmonids’ use of summer rearing and growth habitat, with a subset of studies focusing on foraging position selection and the energetic trade-offs of differential habitat use. To date, however, cost–benefit analyses for most foraging model studies have focused on small sampling areas such as individual habitat units. To address this knowledge gap, we applied a mechanistic foraging model to 22 stream reaches (100–400 m) from two watersheds within the Columbia River Basin. We found a strong, positive correlation (R2 = 0.61, p < 0.001) between predicted carrying capacities and observed fish densities. Predicted proportion of suitable habitat was weakly correlated with observed fish density (R2 = 0.18, p = 0.051), but the mean net rate of energy intake prediction in sampling reaches was not a significant predictor of observed fish biomass. Our results suggest spatial configuration of habitat, in addition to quantity and quality, is an important determinant of habitat use. Further, carrying capacity predicted by the model shows promise as a habitat metric. We also evaluated the feasibility of applying this data-intensive modeling approach in a large-scale monitoring program to examine habitat quality and quantity. Though the approach can be computationally expensive, we feel the model’s ability to integrate physical habitat metrics (e.g., depth, velocity) with important biological considerations like food availability and temperature is a benefit that far outweighs associated costs. We feel this modeling approach has great potential as a tool to help understand habitat use in drift-feeding fishes. © 2016, National Research Council of Canada. All rights reserved.
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 several groups of anadromous fishes, but especially the salmonids, some populations migrate from the ocean to fresh water many months prior to spawning. This "premature migration" reduces growth opportunities at sea, compels them to occupy much less productive freshwater habitats, and exposes them to extremes of flow and temperature, disease, and predation. We first review migration in salmonids and find great variation in timing patterns among and within species, relative to the timing of reproduction. Premature migration is widely distributed among species but not in all populations, and we propose two hypotheses to explain it. First, the fish may be making "the best of a bad situation" by entering early because access to suitable breeding sites is constrained seasonally by flow or temperature regimes, so they sacrifice growing opportunities at sea. Alternatively or additionally, some populations may be "balancing risks and benefits" as they trade off the benefits of growth at sea against the risk of mortality there. In this model, the reduced risk of mortality at sea must be balanced against the risk of mortality in freshwater habitats from thermal stress, disease, and predators. Premature migration may be favored where temperatures and flows are moderate or where lakes provide safety from predators and reduce energetic expenditure. Consistent with this hypothesis, early return is characteristic of larger, older salmonids (that would benefit less from additional time at sea to grow than would smaller fish). Finally, we consider the vulnerability of premature migrants to climate change and selective fisheries. Migration timing is an important part of the portfolio of phenotypic diversity that conveys resilience to species, population complexes, and the fisheries that depend on them. The premature migrants are often especially valued in fisheries and also often of particular conservation concern, and the phenomenon merits further research.
Stable isotope analysis is a powerful method for estimating the impacts animals have on their environment (resource use), revealing their ecological niches.
We demonstrated the use of a stable isotope mixing model for measuring the ecological niches of consumers. In particular, we used the model IsotopeR to estimate the resource use of two species with complex, omnivorous diets: invasive Norway rats from the Aleutian Islands, AK , and American black bears from Yosemite National Park, CA . Marginal posterior distributions for major food sources (for populations, groups and individuals) described the resource axes that partly define the realized niches of these omnivores. We used measures of these resource axes to inform resource management in the Aleutians and Yosemite.
Results from our analyses confirm that coastal rats did not rely on marine birds on rat‐infested islands in the Aleutians. Instead, rats foraged primarily on terrestrial plants and preferred amphipods when they were available. We also use stable isotopes to confirm that plants and acorns are the largest contributors to black bear nutrition in Yosemite and learned that female bears foraged for acorns and pine nuts more heavily than males.
Although it is unclear if Norway rats can maintain viable populations in the Aleutians without access to marine‐derived animal protein, results from our analyses suggest their dependence on such nutrients. In addition, sex‐specific differences in foraging for high‐fat acorns and pine nuts in Yosemite suggest black bear populations in the Sierra Nevada may be limited by the productivity and health of hard mast species. As demonstrated here, stable isotope analysis has wide applicability for investigating the resource use and ecological niches of animals. We anticipate and encourage its rapid development in this fundamental field of ecology.
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 restoration projects. We deployed two metrics at scales ranging from the sub-watershed to ESA listing units; one describes the unit scale match/mismatch between projects and ecological concerns, the other correlates ecological need with need treated by projects across units. Populations with more identified ecological concerns contained more restoration effort, but the frequency of ecological concerns in recovery plans did not correlate with their frequency as restoration targets. Instead, restoration projects were strongly biased towards less expensive types. Many ESA-listed salmon populations (78%) had a good match between need and action noted in their recovery plan, but fewer (31%) matched at the smaller sub-watershed scale. Further, a majority of sub-watersheds contained a suite of projects that matched ecological concerns no better, and often worse, than a random pick of all project types. These results suggest considerable room for gains in restoration funding and placement even in the absence of centralized planning. This analytical approach can be applied to any species for which habitat management is a principle tactic, and in particular can help improve efficiencies in matching identified needs with explicit management actions.
Read More: http://www.esajournals.org/doi/full/10.1890/ES14-00466.1
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.
Reproductive tactics and migratory strategies in Pacific and Atlantic salmonines are inextricably 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 understanding 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 conditional strategies for maturation and, in doing so, demonstrates how flexible life histories can be both heritable and subject to strong environmental influences. We also review evidence that the propensity for freshwater maturation in partially anadromous species is predictable across environmental gradients at geographic and local spatial scales. We note that growth is commonly associated with the propensity for freshwater 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 promote the diversity of maturation phenotypes in Pacific and Atlantic salmonines and caution against underestimating the role of freshwater maturing forms in maintaining the resiliency of these iconic species.
Final version of my PhD dissertation.
Evaluating the effectiveness of instream structures for increasing trout populations is complicated by a paucity of long-term studies. We report on a study spanning 23 years to assess the effect of installing log weirs on stream habitat and trout abundance. Structures were installed in a randomly selected half of a 500 m study reach in six small Colorado, USA, mountain streams in 1988, and habitat and trout abundance and biomass were measured annually from 1987 to 1994. When five of the streams were resampled in 2009, none of the 53 logs had moved, and all but one were functioning properly. Pool volume remained more than three times higher in treatment sections than in adjacent controls, and mean depth was also greater. Adult trout abundance increased rapidly after structures were installed and remained 53% higher in treatment sections than in controls 21 years later. Effects on juvenile trout abundance were not detected, probably because fry recruitment is strongly influenced by effects of snowmelt runoff, which vary annually among basins. This evaluation shows that instream structures placed in small, stable channels can function for more than two decades when properly installed and can cause long-lasting increases in trout abundance when habitat is limiting.
Oncorhynchus mykiss form partially migratory populations with anadromous fish that undergo marine migrations and residents that complete their life cycle in fresh water. Many populations’ anadromous components are threatened or endangered, prompting interest in understanding ecological and evolutionary processes underlying anadromy and residency. In this paper, we synthesize information to better understand genetic and environmental influences on O. mykiss life histories, identify critical knowledge gaps, and suggest next steps. Anadromy and residency appear to reflect interactions among genetics, individual condition, and environmental influences. First, an increasing body of literature suggests that anadromous and resident individuals differ in the expression of genes related to growth, smoltification, and metabolism. Second, the literature supports the conditional strategy theory, where individuals adopt a life history pattern based on their conditional status relative to genetic thresholds along with ultimate effects of size and age at maturation and iteroparity. However, except for a generally positive association between residency and high lipid content plus a large attainable size in fresh water, the effects of body size and growth are inconsistent. Thus, individuals can exhibit plasticity in variable environments. Finally, patterns in anadromy and residency among and within populations suggested a wide range of possible environmental influences at different life stages, from freshwater temperature to marine survival. Although we document a number of interesting correlations, direct tests of mechanisms are scarce and little data exist on the extent of residency and anadromy. Consequently, we identified as many data gaps as conclusions, leaving ample room for future research. © 2015, National Research Council of Canada. All rights reserved.
Although classical ecological theory (e.g., on ideal free consumers) recognizes the potential effect of population density on the spatial distribution of animals, empirical species distribution models assume that species-habitat relationships remain unchanged across a range of population sizes. Conversely, even though ecologicalmodels and experiments have demonstrated the importance of spatial heterogeneity for the rate of population change, we still have no practical method for making the connection between the makeup of real environments, the expected distribution and fitness of their occupants, and the long-termimplications of fitness for population growth. Here, we synthesize several conceptual advances into a mathematical framework using a measure of fitness to link habitat availability/selection to (density-dependent) population growth in mobile animal species. A key feature of this approach is that it distinguishes between apparent habitat suitability and the true, underlying contribution of a habitat to fitness, allowing the statistical coefficients of both to be estimated frommultiple observation instances of the species in different environments and stages of numerical growth. Hence, it leverages data from both historical population time series and snapshots of species distribution to predict population performance under environmental change. We propose this framework as a foundation for building more realistic connections between a population's use of space and its subsequent dynamics (and hence a contribution to the ongoing efforts to estimate a species' critical habitat and fundamental niche). We therefore detail its associated definitions and simplifying assumptions, because they point to the framework's future extensions. We show how the model can be fit to data on species distributions and population dynamics, using standard statistical methods, and we illustrate its application with an individual-based simulation. When contrasted with nonspatial population models, our approach is better at fitting and predicting population growth rates and carrying capacities. Our approach can be generalized to include a diverse range of biological considerations. We discuss these possible extensions and applications to real data.
The distribution and future fate of ectothermic organisms in a warming world will be dictated by thermalscapes across landscapes. That is particularly true for stream fishes and cold-water species like trout, salmon, and char that are already constrained to high elevations and latitudes. The extreme climates in those environments also preclude invasions by most non-native species, so identifying especially cold habitats capable of absorbing future climate change while still supporting native populations would highlight important refugia. By coupling crowd-sourced biological datasets with high-resolution stream temperature scenarios, we delineate network refugia across >250 000 stream km in the Northern Rocky Mountains for two native salmonids-bull trout (BT) and cutthroat trout (CT). Under both moderate and extreme climate change scenarios, refugia with high probabilities of trout population occupancy (>0.9) were predicted to exist (33-68 BT refugia; 917-1425 CT refugia). Most refugia are on public lands (>90%) where few currently have protected status in National Parks or Wilderness Areas (<15%). Forecasts of refuge locations could enable protection of key watersheds and provide a foundation for climate smart planning of conservation networks. Using cold water as a 'climate shield' is generalizable to other species and geographic areas because it has a strong physiological basis, relies on nationally available geospatial data, and mines existing biological datasets. Importantly, the approach creates a framework to integrate data contributed by many individuals and resource agencies, and a process that strengthens the collaborative and social networks needed to preserve many cold-water fish populations through the 21st century.
Published 2015. This article is a U.S. Government work and is in the public domain in the USA.
Recovery criteria, the thresholds mandated by the Endangered Species Act that define when species may be considered for downlisting or
removal from the endangered species list, are a key component of conservation planning in the United States. We recommend improvements in
the definition and scientific justification of recovery criteria, addressing both data-rich and data-poor situations. We emphasize the distinction
between recovery actions and recovery criteria and recommend the use of quantitative population analyses to measure the impacts of threats
and to explicitly tie recovery criteria to population status. To this end, we provide a brief tutorial on the legal and practical requirements and
constraints of recovery criteria development. We conclude by contrasting our recommendations with other alternatives and by describing ways
in which academic scientists can contribute productively to the planning process and to endangered species recovery.
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 (<20%)and that placed wood remains stable for several years, though long-term evaluations of placed wood are rare. The vast majority of studies on wood placement have reported improvements in physical habitat (e.g., increased pool frequency, cover, habitat diversity). Studies that have not reported improvements in physical habitat often found that watershed processes (e.g., sediment, hydrology, water quality)had not been addressed. Finally, most evaluations of fish response to wood placement have shown positive responses for salmonids, though few studies have looked at long-term watershed-scale responses or studied a wide range of species. © 2015, National Research Council of Canada. All rights reserved.
Fish communities in high-elevation, Rocky Mountain streams consist of only one or a few trout species, so these streams are ideal for quantifying how physical habitat manipulation influences population biology. Managers often alter habitat structure in hopes of increasing the number of size of fish in a population, but this practice has not been rigorously evaluated, and the mechanisms involved are not well understood. We measured fish abundance and habitat conditions in each half of 500-m study reaches in six streams for 2 yr before and 6 yr after installing 10 low log weirs in a randomly designated half (treatment section). Mean depth, pool volume, total cover, and the proportion of fine substrate particles in the stream bed increased in treatment sections within 1 to 2 years, whereas habitat in adjacent controls remained unchanged. Abundance and biomass of adult fish, but not juveniles, increased in treatments relative to controls in all streams. Recaptures of trout that were individually tagged and others that were batch marked revealed that immigration was primarily responsible for increased adult abundance and biomass, whereas no biologically significant differences occurred for recruitment, survival, or growth. Few (
Populations of some Pacific and Atlantic salmon species contain a mixture of anadromous and non-anadromous individuals. Because of an increased interest in potential demographic and genetic advantages of populations exhibiting mixed migratory strategies, we provide a framework for investigating the ecological and evolutionary significance of freshwater maturation in salmonines. For convenience, we first independently consider hypotheses related to ultimate and proximate factors underlying freshwater maturation. We evaluate several evolutionary hypotheses to explain patterns of freshwater maturation among and within salmonines including phylogenetic history, irreversible evolutionary transitions within species (e.g., vicariance), geographic variation in selective pressures, and contemporary reductions in genetic variability in reactions norms (e.g., effects of domestication selection). Ecological hypotheses for proximate mechanisms underlying freshwater maturation include environmental constraints to freshwater maturation, interspecific interactions, and environmental stochasticity (e.g., dynamic vs. stable environments). We then consider the interaction of ecological and evolutionary processes underlying patterns of freshwater maturation and discuss how they influence demographic and genetic resilience of populations. Our goals are to elucidate patterns of freshwater maturation among and within species of salmonines, identify potential conservation actions that promote population recovery and resiliency by facilitating diversity in life history expression, and identify critical knowledge gaps.
Steelhead Oncorhynchus mykiss from several of the world's rivers display the half‐pounder life history, a variant characterized by an amphidromous (and, less often, anadromous) return to freshwater in the year of initial ocean entry. We evaluated factors related to expression of the half‐pounder life history in wild steelhead from the lower Klamath River basin, California. We also evaluated fitness consequences of the half‐pounder phenotype using a simple life history model that was parameterized with our empirical data and outputs from a regional survival equation. The incidence of the half‐pounder life history differed among subbasins of origin and smolt ages. Precocious maturation occurred in approximately 8% of half‐pounders and was best predicted by individual length in freshwater preceding ocean entry. Adult steelhead of the half‐pounder phenotype were smaller and less fecund at age than adult steelhead of the alternative (ocean contingent) phenotype. However, our data suggest that fish of the half‐pounder phenotype are more likely to spawn repeatedly than are fish of the ocean contingent phenotype. Models predicted that if lifetime survivorship were equal between phenotypes, the fitness of the half‐pounder phenotype would be 17–28% lower than that of the ocean contingent phenotype. To meet the condition of equal fitness between phenotypes would require that first‐year ocean survival be 21–40% higher among half‐pounders in freshwater than among their cohorts at sea. We concluded that continued expression of the half‐pounder phenotype is favored by precocious maturation and increased survival relative to that of the ocean contingent phenotype.
Received October 23, 2013; accepted February 4, 2014
This study considered whether different population viability analyses give similar estimates of extinction risk across management contexts. We compared the performance of population viability analyses developed by numerous scientific teams to estimate extinction risk of anadromous Pacific salmonids listed under the U.S. Endangered Species Act and challenged each analysis with data from 34 populations. We found variation in estimated extinction risk among analytical techniques, which was driven by varying model assumptions and the inherent uncertainty of risk forecasts. This result indicates that the scientific teams developed techniques that perform differently. We recommend that managers minimize uncertainty in risk estimates by using multiple models tailored to the local ecology. Assessment of relative extinction risk was less sensitive to model assumptions than was assessment of absolute extinction risk. Thus, the former method is better for comparing population status and raises caution about conclusions regarding absolute extinction risk.
Received October 18, 2012; accepted July 3, 2013
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.
Evidence suggests Snake River stream-type Chinook salmon (Oncorhynchus tshawytscha) experience substantial delayed mortality in the marine environment as a result of their outmigration experience through the Federal Columbia River Power System (FCRPS). We analyzed mortality patterns using methods that incorporated downriver reference populations passing fewer dams, and temporal approaches that were independent of reference populations. Our results from the alternative spatial and temporal methods consistently corroborated with spawner–recruit residuals and smolt-to-adult survival rate data sets, indicating that Snake River salmon survived about one quarter as well as the reference populations. Temporal analysis indicated that a high percentage (76%) of Snake River juvenile salmon that survived the FCRPS subsequently died in the marine environment as a result of their outmigration experience. Through this and previous studies, it is evident that delayed hydrosystem mortality increases with the number of powerhouse passages and decreases with the speed of outmigration. Therefore, a promising conservation approach would be to explore management experiments that evaluate these relationships by increasing managed spill levels at the dams during the spring migration period.
Instream wood is a driver of geomorphic change in low-order streams, frequently altering morphodynamic processes. Instream wood is a frequently measured component of streams, yet it is a complex metric, responding to ecological and geomorphic forcings at a variety of scales. Here we seek to disentangle the relative importance of physical and biological processes that drive wood growth and delivery to streams across broad spatial extents. In so doing, we ask two primary questions: (1) is riparian vegetation a composite variable that captures the indirect effects of climate and disturbance on instream wood dynamics? (2) What are the direct and indirect relationships between geomorphic setting, vegetation, climate, disturbance, and instream wood dynamics? We measured riparian vegetation composition and wood frequency and volume at 720 headwater reaches within the American interior Pacific Northwest. We used ordination to identify relationships between vegetation and environmental attributes, and subsequently built a structural equation model to identify how climate and disturbance directly affect vegetation composition and how vegetation and geomorphic setting directly affect instream wood volume and frequency. We found that large wood volume and frequency are directly driven by vegetation composition and positively correlated to wildfire, elevation, stream gradient, and channel bankfull width. Indicator species at reaches with high volumes of wood were generally long-lived, conifer trees that persist for extended durations once delivered to stream habitats. Wood dynamics were also indirectly mediated by factors that shape vegetation: wildfire, precipitation, elevation, and temperature. We conclude that wood volume and frequency are driven by multiple interrelated climatic, geomorphic, and ecological variables. Vegetation composition and geomorphic setting directly mediate indirect relationships between landscape environmental processes and instream large wood. Where climate or geomorphic setting preclude tree establishment, reaches may remain naturally depauperate of instream wood unless wood is transported from elsewhere in the stream network.
The habitat complexity of a riverine ecosystem influences the bioenergetics of drift feeding fish. We coupled hydrodynamic and bioenergetic models to assess the influence of habitat complexity generated by large woody debris (LWD) on the growth potential of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river that lacked large wood. Simulations indicated how LWD diversified the flow field, creating pronounced velocity gradients, which enhanced fish feeding and resting activities at the sub-meter scale. Fluid drag created by individual wood structures increased under higher wood loading amounts, leading to a 5–19% reduction in the reach-averaged velocity. The reach-scale growth potential was asymptotically related to wood loading, suggesting that the river became saturated with LWD and additional loading would produce minimal benefit for the configurations we simulated. In the scenario we analyzed for illustration, LWD additions could quadruple the potential growth area available before that limit was reached for the configurations selected for demonstration. Wood depletion in the world's rivers has been documented extensively, leading to widespread attempts by river managers to reverse this trend by adding wood to simplified aquatic habitats. However, systematic prediction of the effects of wood on fish growth has not been previously accomplished. We offer a quantitative approach for assessing the influence of wood on habitat potential for fish growth at the microhabitat and reach-scales.
Accurately measuring productive capacity in streams is challenging, and field methods have generally focused on the limiting role of physical habitat attributes (e.g. channel gradient, depth, velocity, substrate). Because drift-foraging models uniquely integrate the effects of both physical habitat (velocity and depth) and prey abundance (invertebrate drift) on energy intake for drift-feeding fishes, they provide a coherent and transferable framework for modelling individual growth that includes the effects of both physical habitat and biological production. Despite this, drift-foraging models have been slow to realize their potential in an applied context. Practical applications have been hampered by difficulties in predicting growth (rather than habitat choice), and scaling predictions of individual growth to reach scale habitat capacity, which requires modelling the partitioning of resources among individuals and depletion of drift through predation. There has also been a general failure of stream ecologists to adequately characterize spatial and temporal variation in invertebrate drift within and among streams, so that sources of variation in this key component of drift-foraging models remain poorly understood. Validation of predictions of habitat capacity have been patchy or lacking, until recent studies demonstrating strong relationships between drift flux, modeled Net Energy Intake, and fish biomass. Further advances in the practical application of drift-foraging models will require i) a better understanding of the factors that cause variation in drift, better approaches for modelling drift, and more standardized methods for characterizing it; ii) identification of simple diagnostic metrics that correlate strongly with more precise but time-consuming bioenergetic assessments of habitat quality; and iii) a better understanding of how variation in drift-foraging strategies are associated with other suites of co-evolved traits that ecologically differentiate taxa of drift-feeding salmonids.
In this paper we review drift-feeding models for stream salmonids. We assess their historical development and current state, and we propose areas for future research. Drift-feeding models serve as the critical input for energetics-based habitat selection and habitat quality models, which have recently begun to see widespread use for predicting salmonid distribution, growth and abundance. We use a bibliometric approach to find drift-feeding model publications, especially those citing three landmark papers that began the quantification of drift feeding by stream fish (Fausch 1984; Hughes and Dill 1990; Hill and Grossman 1993). Subsequent drift-feeding models have largely been built upon these models. Research effort has focused on model development and applications but model testing has been neglected. To date, the only rigorous test of a drift-feeding model (Hughes et al. 2003) identified several limitations and violations of model assumptions. The most important limitation was that prey capture- and gross energy intake rates were overestimated by a factor of two, due largely to poor predictions of prey detection probabilities. Consequences of error in drift-feeding models, and consequently in the habitat selection/quality models that employ them, are greater for applications aimed at predicting growth and abundance than they are for predicting distribution. Research effort on a broad front is needed to advance both drift-feeding models and habitat selection/quality models, including: further development of drift-foraging theory, revision and testing of drift-feeding models (specifically new, functional prey detection and interception sub-models), and revision of habitat selection/quality models to incorporate spatial, temporal, and flow-dependent variation in drift concentration.
Pacific Northwest Chinook, Oncorhynchus tshawytscha, have exhibited a high degree of variability in smolt-to-adult survival over the past three decades. This variability is summarized for 22 Pacific Northwest stocks and analyzed using generalized linear modeling techniques. Results indicate that survival can be grouped into eight distinct regional clusters: (1) Alaska, Northern BC and North Georgia Strait; (2) Georgia Strait; (3) Lower Fraser River and West Coast Vancouver Island; (4) Puget Sound and Hood Canal; (5) Lower Columbia Tules; (6) Columbia Upriver Brights, Willamette and Cowlitz; (7) Oregon and Washington Coastal; and (8) Klamath River and Columbia River Summers. Further analysis for stocks within each of the eight regions indicates that local ocean conditions following the outmigration of smolts from freshwater to marine areas had a significant effect on survival for the majority of the stock groups analyzed. Our analyses of the data indicate that Pacific Northwest Chinook survival covaries on a spatial scale of 350–450 km. Lagged time series models are presented that link large-scale tropical Pacific conditions, intermediate-basin scale northeastern Pacific conditions, and local sea surface temperatures to survival of Pacific Northwest stocks.
The Physical Habitat Simulation System (PHABSIM) was developed in the 1970s to fill an important void in instream flow assessment. Although considerable progress has been made in ecological modeling since the 1970s, there has been little change in instream flow assessment. PHABSIM has two general problems. First, PHABSIM is a habitat selection model (HSM)—but not a good one: it no longer conforms to standard practices in the wider fields of ecological and wildlife modeling, especially by using inappropriate spatial scales and outdated methods for modeling habitat preference and by producing output that lacks clear meaning. Second, HSMs, in general, are not well suited for many instream flow decisions. HSMs cannot consider variation in flow over time, whereas dynamic flow regimes are now considered essential, and HSMs do not make testable predictions of fish population responses. Alternatives to PHABSIM include analyses based on explicit understanding of species ecology, individual-based models, and more powerful modern habitat selection modeling methods.
To examine seasonal and spatial factors affecting prey consumption by Oncorhynchus trout, we examined trout diet from mainstem and tributary sites at Hinkle Creek, Oregon. Benthic invertebrate densities were similar across seasons and did not differ between tributaries and the mainstem. Fluctuations in diet followed seasonal changes in invertebrate sizes and abundances. Average prey biomass consumed was positively correlated with fish size. Consumption rates were high in spring and summer but fell significantly in fall when fewer and smaller prey were eaten. A switch in consumption from 36% terrestrial prey biomass in spring to 85% in summer coincided with an increase in terrestrial prey size and a decrease in benthic prey size. Location within the watershed also affected prey consumption. Despite similarities in diet composition, tributary trout consumed somewhat more biomass than trout in the mainstem but grew relatively slower. Because stream fishes such as Oncorhynchus trout feed opportunistically on varied prey, studies incorporating multiple seasons and stream types are important to understanding energy exchanges between terrestrial and aquatic ecosystems.
We compared a process-based invertebrate drift and drift-feeding net rate of energy intake (NREI) model and a traditional hydraulic-habitat model (using the RHYHABSIM [River Hydraulics and Habitat Simulation] software program) for predicting the flow requirements of 52-cm Brown Trout Salmo trutta in a New Zealand river. Brown Trout abundance predicted by the NREI model for the constant drift concentration–flow scenarios were asymptotic or linear, depending on drift concentration, increasing through the mean annual low flow (MALF; 17 m3/s). However, drift concentration increased with flow, consistent with passive entrainment. The predicted fish abundance–flow relationship based on flow-varying drift concentration increased logistically, and more steeply, with flow through the MALF and beyond. Predictions for the relationship between weighted useable area (WUA) and flow were made for three sets of drift-feeding habitat suitability criteria (HSC) developed on three midsized and one large New Zealand river (flow at sampling was 2.8–4.6 m3/s and ~100 m3/s, respectively) and the South Platte River, Colorado (flow at sampling, 7–18 m3/s). The midsized-river HSC ascribe lower suitability to water velocities > 0.6 m/s. They predicted WUA peaking at 10–11 m3/s, well below the MALF. The WUA–flow relationships for the two large-river HSC were asymptotic at about 22 m3/s. Overall, WUA appears to underestimate the flow needs of drift-feeding salmonids. The NREI model showed that assessing flow needs of drift-feeding fish is more complex than interpreting a WUA–flow relationship based only on physical habitat suitability. The relationship between predicted fish abundance and flow is an emergent property of flow-dependent drift-foraging dynamics interacting with flow-dependent drift concentration and drift flux, local depletion of drift by feeding fish, and flow-related replenishment of drift from the bed and dispersion. It is time that the principles and predictions of drift–NREI models influence assessments of habitat capacity and instream flow needs of drift-feeding fish.Received April 10, 2015; accepted November 10, 2015 Published online April 27, 2016
Frameworks for assessing geomorphic river condition constitute a core part of the river management process, providing a critical platform for environmental decision‐making and associated actions. The evolution of approaches for assessing the geomorphic (also called physical, morphological, or hydromorphological) condition of rivers has shifted from a design and development phase in the late‐1990s and early 2000s to application and use of approaches for assessment, monitoring, and rehabilitation decision making. In this paper I review the core geomorphic principles that are embedded in more sophisticated, process‐based frameworks, and demonstrate how the information generated through use of these frameworks can be used to guide management choices, change management activities or opt‐out of management activities as part of precautionary river management practice. I propose that a key challenge now faced by geomorphologists and managers is to move beyond the development of more new frameworks, and consolidate efforts to use, test, and adapt existing approaches and datasets to achieve river management visions and objectives framed around improving river condition. WIREs Water 2015, 2:649–667. doi: 10.1002/wat2.1100
This article is categorized under: Water and Life > Conservation, Management, and Awareness
Engineering Water > Planning Water
In recent years an increasing share of fishery management resources has been committed to alteration offish habitat with artificial stream structures. We evaluated rates and causes of physical impairment or failure for 161 fish habitat structures in 15 streams in southwest Oregon and southwest Washington, following a flood of a magnitude that recurs every 2–10 years. The incidence of functional impairment and outright failure varied widely among streams; the median failure rate was 18.5% and the median damage rate (impairment plus failure) was 60%. Modes of failure were diverse and bore no simple relationship to structure design. Damage was frequent in low-gradient stream segments and widespread in streams with signs of recent watershed disturbance, high sediment loads, and unstable channels. Comparison of estimated 5–10-year damage rates from 46 projects throughout western Oregon and southwest Washington showed high but variable rates (median, 14%; range, 0–100%) in regions where peak discharge at 10-year recurrence intervals has exceeded 1.0 m3·s–1·km–2. Results suggest that commonly prescribed structural modifications often are inappropriate and counterproductive in streams with high or elevated sediment loads, high peak flows, or highly erodible bank materials. Restoration of fourth-order and larger alluvial valley streams, which have the greatest potential for fish production in the Pacific Northwest, will require reestablishment of natural watershed and riparian processes over the long term.
The Columbia River Basin (Basin) is located in the Pacific Northwest, United States. The 370 hydroelectric dams in the Basin provide the Northwest with many services including hydropower generation, flood control, agricultural irrigation, and navigation. The basin also provides habitat for a variety of species. Balancing the energy demands with the needs of fish and wildlife, especially anadromous salmonids, is a daunting task. Through the implementation of the Pacific Northwest Electric Power Planning and Conservation Act (Power Act) the Northwest Power and Conservation Council in collaboration with state, federal, tribal, and non-governmental partners attempts to address the needs of fish and wildlife with that of hydropower generation. The implementation is challenging as the Basin’s ecosystem is stressed by societal demands and the resulting environmental impacts. We will discuss ongoing challenge of meeting the demands for hydropower generation and of the basin’s fish species
Like many rivers and streams in forests of the Pacific Northwest, California north coast rivers and streams have been depleted of downed wood through timber harvest and direct wood removal. Due to the important role of wood in creating and maintaining salmonid habitat, wood augmentation has become a common element of stream restoration. Restoration efforts in North America often focus on building anchored, engineered wood structures at the site scale; however, these projects can fail to meet restoration goals at the watershed scale, do not closely mimic natural wood loading processes or dynamics, and can be expensive to implement. For critically imperiled populations of Coho Salmon Oncorhynchus kisutch in California, there is a strong impetus to achieve as much habitat restoration as possible in priority watersheds in the shortest time and with limited resources, so cost‐efficient techniques are necessary. In this multi‐site project, we investigated unanchored techniques for wood loading to evaluate cost and contribution to salmonid habitat in Mendocino County, California. Over a period of 6 years, 72.4 km of stream were treated with 1,973 pieces of strategically placed wood. We found that unanchored wood loading techniques were much less costly than commonly used anchored techniques, reliably improved habitat, and retained wood at high rates (mean = 92%) in small‐ to moderate‐sized streams, at least over the short term (<6 years). The average cost of design and construction for the unanchored projects was US$259 per log, equivalent to 22% of the cost associated with the anchored wood augmentation methods examined here. Our results suggest that this unanchored wood loading approach has the potential to increase the pace and scale at which wood augmentation projects are implemented in the Pacific Northwest and beyond.
Received January 22, 2014; accepted June 25, 2014
To examine the extent to which stream-resident coastal cutthroat trout (Oncorhynchus clarki) are limited by food and cover, we manipulated these two factors in a 2 × 2 design using enclosures containing 1-year-old trout in two streams. During summer, fish receiving food additions experienced an average growth rate of 1.73% body mass·day–1 compared with a rate of 0.022 for unfed fish (ambient food supply only), indicating marked food limitation. The addition of cover decreased mortality by approximately 50% in one stream, but survival was high both with and without cover in the other. There was no interaction of food and cover on growth or survival. Emigration rates were low and were not strongly affected by either factor. We also used mark–recapture modeling to examine whether the 48% greater mass of fed fish at the end of the experiment improved survival over winter. Fed fish were still 46% larger than unfed fish by the next spring, but overwinter survival was not explained by body size. Our results show that, during summer, food availability can limit trout growth, and cover, by mediating predation, can limit survival.Afin de déterminer dans quelle mesure le gîte et la nourriture peuvent être des facteurs limitants pour les truites fardées côtières (Oncorhynchus clarki) habitant les cours d'eau de la côte, nous avons établi un plan d'expérience de type 2 × 2 pour manipuler ces facteurs dans des enclos contenant des poissons de 1 an dans deux cours d'eau. En été, les poissons qui ont reçu des suppléments de nourriture avaient un taux de croissance moyen de 1,73 % de la masse totale·jour–1, alors que les poissons qui n'ont eu accès qu'à la nourriture ambiante avaient un taux de 0,022, ce qui indique que la nourriture est un facteur limitant important. L'addition de gîtes a réduit la mortalité d'environ 50 % dans un des cours d'eau, mais, dans l'autre, la survie est restée élevée avec ou sans les gîtes additionnels. Il n'y a pas eu d'effet combiné de la nourriture et du gîte sur la croissance ou la survie. Les taux d'émigration étaient bas et n'étaient pas affectés ni par l'un, ni par l'autre des facteurs. Une modélisation de type marquage–recapture nous a permis de voir si la masse accrue de 48 % à la fin de l'expérience chez les poissons nourris en supplément augmentait leur survie en hiver. Les poissons nourris avaient une masse supérieure de 46 % à celle des poissons non nourris le printemps suivant, mais la survie à l'hiver n'était pas reliée à la taille des poissons. Nos résultats indiquent qu'en été la disponibilité de la nourriture peut limiter la croissance des truites fardées et que le gîte peut limiter la survie en affectant la prédation.[Traduit par la Rédaction]