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Joseph R. Benjamin

Publications and source records attributed to Joseph R. Benjamin.

At least 19 recordsLinked to original sources
USGS2025

Effects of riparian forest thinning on resident salmonid fishes in coastal northern California catchments

Resource managers are interested in whether thinning second-growth forests may be a viable restoration strategy for stream and riparian habitats, but may be concerned about the potential impacts that increases in stream temperature associated with riparian thinning treatments may have on cold-water salmonid fishes. We evaluated the effects of riparian forest thinning on resident populations of coastal cutthroat trout ( Oncorhynchus clarkii clarkii ) in coastal northern California catchments using a manipulative field experiment with a replicated before-after-control-impact design (pre-treatment data collected in 2016, thinning treatments occurred in 2017, and post-treatment data collected in 2018). Experimental thinning treatments reduced riparian shade by 20%–30% along five 150–200 m stream reaches. To provide a process-based evaluation of the implications of riparian thinning for coastal cutthroat trout, we combined seasonal observations of trout density, biomass, and growth with bioenergetics modelling. Cutthroat trout density increased by 8%–31% and biomass increased by 27%–111% in thinned reaches 1 year post-treatment, but responses varied widely across sites and seasons so did not always differ statistically. Growth rates of cutthroat trout varied more among seasons than among reach types (upstream reference, thinned, and downstream), peaking in spring and overwinter relative to summer. Bioenergetics modelling indicated that cutthroat trout responded to thinning-induced increases in stream temperature and shifts in prey energy density via higher consumption rates (i.e., fish fed more frequently) in thinned reaches. Additionally, reach-scale consumption estimates indicated that the energy intake of cutthroat trout increased at the population level in thinned reaches. However, thinned reaches exhibited relatively small changes in consumption, suggesting that riparian thinning was unlikely to enhance growth opportunities for cutthroat trout, supporting our empirical growth observations. Collectively, our field experiment suggests that salmonid fishes may be resilient to thinning second-growth riparian forests when treatments do not substantially increase water temperatures. Moreover, our results highlight that pairing empirical data with bioenergetics modelling can provide valuable insights into the mechanisms driving fish responses to riparian forest restoration.

California↗
USGS2025

New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application

Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and conservation. We used Pacific lamprey ( Entosphenus tridentatus ) as a case study to highlight the utility of this model. We applied a global sensitivity analysis to explore the importance of individual life stage parameters to overall population size, and to better understand the implications of existing gaps in knowledge. We also provided example analyses of selected management scenarios (dam passage, fish translocations, and hatchery additions) influencing Pacific lamprey in fresh water. These applications illustrate how the model can be applied to inform conservation efforts. This tool will provide new capabilities for users to explore their own questions about lamprey biology and conservation. Simulations can hone hypotheses and predictions, which can then be empirically tested in the real world.

PLoS ONE↗
USGS2025

A partner-driven decision support model to inform the reintroduction of bull trout

Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout ( Salvelinus confluentus ) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.

Washington↗
USGS2025

Linking fire, food webs, and fish in stream ecosystems

As wildfire regimes shift, resource managers are concerned about potential threats to aquatic ecosystems and the species they support, especially fishes. However, predicting fish responses can be challenging because wildfires affect aquatic ecosystems via multiple pathways. Application of whole-ecosystem approaches, such as food web modeling, can act as heuristic tools that offer valuable insights that account for these different mechanisms. We applied a dynamic food web simulation model that mechanistically linked stream trophic dynamics to the myriad effects that wildfires can have on aquatic and riparian ecosystems at a local stream reach-scale. We simulated how wildfires of different severity may influence short- (months to years) and long-term (years to decades) periphyton, aquatic invertebrate, and fish biomass dynamics in forested headwater streams of the western Pacific Northwest (USA). In many cases, wildfire increased modeled periphyton, invertebrate, and fish biomass over both short- and long-time periods. However, modeled responses varied extensively in their direction (that is, positive or negative), magnitude, and duration depending on fire severity, time since fire, and trophic level. The shapes of these response trajectories were especially sensitive to predicted wildfire effects on water temperature, canopy cover, riparian shading, and instream turbidity. Model simulations suggest a single fire could result in a wide range of aquatic ecosystem responses, especially in watersheds with mixed burn severity. Our analysis highlights the utility of whole-ecosystem approaches, like food web modeling, as heuristic tools for improving our understanding of the mechanisms linking fire, food webs, and fish and for identifying contexts where fires could have deleterious impacts on fishes.

Oregon, Washington↗
USGS2024

Food-web dynamics of a floodplain mosaic overshadow the effects of engineered logjams for Pacific salmon and steelhead

Food webs vary in space and time. The structure and spatial arrangement of food webs are theorized to mediate temporal dynamics of energy flow, but empirical corroboration in intermediate-scale landscapes is scarce. River-floodplain landscapes encompass a mosaic of aquatic habitat patches and food webs, supporting a variety of aquatic consumers of conservation concern. How the structure and productivity of these patch-scale food webs change through time, and how floodplain restoration influences their dynamics, are unevaluated. We measured productivity and food-web dynamics across a mosaic of main-channel and side-channel habitats of the Methow River, WA, USA, during two study years (2009–2010; 2015–2016) and examined how food webs that sustained juvenile anadromous salmonids responded to habitat manipulation. By quantifying temporal variation in secondary production and organic matter flow across nontreated river-floodplain habitats and comparing that variation to a side channel treated with engineered logjams, we jointly confronted spatial food-web theory and assessed whether food-web dynamics in the treated side channel exceeded natural variation exhibited in nontreated habitats. We observed that organic matter flow through the more complex, main-channel food web was similar between study years, whereas organic matter flow through the simpler, side-channel food webs changed up to ~4-fold. In the side channel treated with engineered logjams, production of benthic invertebrates and juvenile salmonids increased between study years by 2× and 4×, respectively; however, these changes did not surpass the temporal variation observed in untreated habitats. For instance, juvenile salmonid production rose 17-fold in one untreated side-channel habitat, and natural aggregation of large wood in another coincided with a shift to community and food-web dominance by juvenile salmonids. Our findings suggest that interannual dynamism in material flux across floodplain habitat mosaics is interrelated with patchiness in food-web complexity and may overshadow the ecological responses to localized river restoration. Although this dynamism may inhibit detection of the ecological effects of river restoration, it may also act to stabilize aquatic ecosystems and buffer salmon and other species of conservation concern in the long term. As such, natural, landscape-level patchiness and dynamism in food webs should be integrated into conceptual foundations of process-based, river restoration.

Washington↗
USGS2024

Assisted migration of coho salmon: Influences of passage and habitat availability on population dynamics

Assisted migration is a means of introducing a species into a previously unoccupied area. Although this idea is relatively new for many species, there are many extant examples involving fish that can be instructive. We studied a case of assisted migration where upstream access of migrating adult coho salmon Oncorhynchus kisutch over a naturally impassible barrier was established through construction of fish ladders. Although these passage structures have successfully allowed coho salmon to colonize upstream locations, managers had concerns regarding how efficiently these structures passed fish, as well as questions regarding access to specific upstream habitats, and passage barriers further upstream. To address these concerns, we developed a stage-based population model to explore: (1) influences of passage over structures, (2) rearing habitats upstream of the structures, and (3) consequences of additional barriers to passage in the system. Model simulations suggest high fish passage at the ladders was associated with the highest smolt and adult abundance of coho salmon. The importance of passage was strongly influenced by juveniles rearing in a lake, where increased lake rearing at each passage scenario increased abundance of smolts and adults. Opening habitat further upstream was estimated to increase adult and smolt abundance up to 12%. Results of model simulations also helped to identify uncertainties that could be evaluated further (e.g., juvenile rearing in the lake). In general, our findings point to the importance of considering a full range of processes that can drive expected outcomes for assisted migration.

Oregon↗
USGS2024

New technology for an ancient fish: A lamprey life cycle modeling tool with an R Shiny application

Lampreys (Petromyzontiformes) are an ancient group of fishes with complex life histories. We created a life cycle model that includes an R Shiny interactive web application interface to simulate abundance by life stage. This will allow scientists and managers to connect available demographic information in a framework that can be applied to questions regarding lamprey biology and conservation. We used Pacific lamprey (Entosphenus tridentatus) as a case study to highlight the utility of this model. We applied a global sensitivity analysis to explore the importance of individual life stage parameters to overall population size, and to better understand the implications of existing gaps in knowledge. We also provided example analyses of selected management scenarios (dam passage, fish translocations, and hatchery additions) influencing Pacific lamprey in fresh water. These applications illustrate how the model can be applied to inform conservation efforts. This tool will provide new capabilities for users to explore their own questions about lamprey biology and conservation. Simulations can hone hypotheses and predictions, which can then be empirically tested in the real world.

EcoEvoRxiv↗
USGS2023

Co-production of models to evaluate conservation alternatives for a threatened fish in a rapidly changing landscape

Reintroductions are one means of managing species distributions, but the feasibility of such efforts is uncertain. Here we consider reintroduction for threatened bull trout ( Salvelinus confluentus ) that currently occupy a small fraction of historically occupied habitats in the upper Klamath River basin owing to climate warming and human modifications of ecosystems. We engaged stakeholders across multiple organizations to co-produce a decision support model that estimated the potential of reintroduction to establish new populations and persistence of donor populations. Stakeholders identified recipient and donor populations, strategy (e.g., artificial propagation, translocation), number of individuals, and life stage of bull trout. The most optimal decision for reintroduction was artificial propagation of 10,000 fry into Annie Creek. This strategy may have negative consequences on donor populations, with the exception of Sun Creek, which was resilient to simulated removal of bull trout. Donor populations and recipient streams identified as most feasible were generally consistent across all of these scenarios. During model development, however, an unexpected and intense wildfire affected half of the streams considered and may have dramatically impacted donor populations. With models in hand from the initial feasibility assessment, we adapted them to further evaluate the potential of supplementation following this massive disturbance. Overall, results of this study indicate the value of developing co-produced tools that can be rapidly adapted to evaluate the consequences of whole-system transformations in near-real-time assessments.

Oregon↗
USGS2023

Climate vulnerability for a desert fish: Integrating hydrologic exposures, adaptive capacity, and growth potential

Climate vulnerability can be evaluated by multiple organismal responses. We developed a climate vulnerability framework focused on growth potential of redband trout (Oncorhynchus mykiss newberri). We employed a bioenergetics model to evaluate spatial variability in growth potential in relation to constraints on body size imposed by stream flow, physiological responses linked to variable thermal regimes, and variation in physiological adaptive capacity inferred from field respirometry. Results indicate that maximum size (g) of redband trout increases with stream discharge. Growth potential is strongly linked to body size, with smaller individuals performing better relative to larger fish in cooler thermal regimes. Annual patterns of growth varied among sites and were related to body size and physiological adaptive capacity. Putatively cold-adapted fish were more likely to exhibit bimodal growth with peaks in spring and autumn, whereas warm-adapted fish exhibit a summer peak in growth potential. These findings offer insights into how climate vulnerability of stream-living fish can be conditioned on both stream flow and thermal regimes, and the potential for physiological adaptive capacity to influence vulnerability.

Canadian Journal of Fisheries and Aquatic Sciences↗
USGS2022

Resist, accept, and direct responses to biological invasions: A social–ecological perspective

Biological invasions represent an important and unique case of ecological transformation that can strongly influence species and entire ecosystems. Challenges in managing invasions arise on multiple fronts, ranging from diverse and often divergent values associated with native and introduced species, logistical constraints, and transformation via other change agents (e.g., climate and land-use change). We address biological invasions considering the Resist-Accept-Direct (RAD) framework for addressing ecological transformation. Because RAD is focused on decisions, we address both social and ecological factors that influence preferences for decision alternatives. We address social factors first as these can constrain the range of alternatives considered in an ecological context. Next, we address ecological dynamics by modeling trajectories from RAD alternatives in a two-species scenario involving impacts of introduced brook trout ( Salvelinus fontinalis ) on native bull trout ( S. confluentus ). Results reveal that decision alternatives aligned with each of the major components of RAD can produce positive outcomes. In a management context, these findings highlight the value of investing in early engagement to fully identify decision alternatives, formalizing models of system dynamics to understand ecological trajectories, and applying this knowledge to set the stage for longer term efforts to address biological invasions.

Fisheries Management and Ecology↗
USGS2022

Pathways of productivity and influences on top consumers in forested streams

Forested stream ecosystems involve complex physical and biotic pathways that can influence fish in numerous ways. Consequently, the responses of fish communities to disturbance can be difficult to understand. In this study, we employed a food web model that links biotic (e.g., physiology, predator–prey interactions) and abiotic (e.g., temperature, sunlight) attributes to address fish responses to changes in stream-riparian ecosystems. We modeled responses to food web dynamics in four streams, using scenarios that included responses to riparian disturbance, climate change, and shifts in top consumers. The two consumers we focused on were coastal cutthroat trout ( Oncorhynchus clarkii clarkii ) and sculpin ( Cottus spp., collectively treated as a functional group) . We found the responses to environmental changes varied by fish species and among streams, and that responses were not independent due to exploitative interspecific competition. Simulations based on long-term data indicated that coastal cutthroat trout were responsive to changes in allochthonous resources including terrestrial detritus and invertebrates, whereas sculpin were more responsive to changes to autochthonous resources that included, periphyton and aquatic invertebrates. These results may be, in part, a consequence of species-specific foraging behavior. Trout have a higher propensity to drift feed and therefore receive a substantial subsidy from terrestrial invertebrates, whereas sculpin feed mostly on aquatic insects on the streambed. Simulations of changes in summer temperature and stream discharge suggest decreased biomass of both fish species because of physiological constraints on invertebrate prey which reduce fish foraging opportunities. Exploitative competition also may be important in fish responses: when one fish taxon was removed, the other showed increased biomass. Although the pattern of simulation results was consistent across the four streams, the magnitude of change varied among streams. Streams with food webs fueled by multiple energy sources may be more resilient to changes to riparian forests and climate. Through application of a systems model, we gained insights into pathways of productivity for fish in forested stream ecosystems that provide understanding of processes that influence fish and streams, as well as implications for management of both.

Forest Ecology and Management↗
USGS2020

Magnitude and direction of stream–forest community interactions change with timescale

Networks of direct and indirect biotic interactions underpin the complex dynamics and stability of ecological systems, yet experimental and theoretical studies often yield conflicting evidence regarding the direction (positive or negative) or magnitude of these interactions. We revisited pioneering data sets collected at the deciduous forested Horonai Stream and conducted ecosystem‐level syntheses to demonstrate that the direction of direct and indirect interactions can change depending on the timescale of observation. Prior experimental studies showed that terrestrial prey that enter the stream from the adjacent forest caused positive indirect effects on aquatic invertebrates during summer by diverting fish consumption. Seasonal and annual estimates of secondary production and organic matter flows along food web pathways demonstrate that this seasonal input of terrestrial invertebrate prey increases production of certain fish species, reversing the indirect effect on aquatic invertebrates from positive at the seasonal timescale to negative at the annual timescale. Even though terrestrial invertebrate prey contributed 54% of the annual organic matter flux to fishes, primarily during summer, fish still consumed 98% of the aquatic invertebrate annual production, leading to top‐down control that is not revealed in short‐term experiments and demonstrating that aquatic prey may be a limiting resource for fishes. Changes in the direction or magnitude of interactions may be a key factor creating nonlinear or stabilizing feedbacks in complex systems, and these dynamics can be revealed by merging experimental and comparative approaches at different scales.

Ecology↗
USGS2020

Thermal heterogeneity, migration, and consequences for spawning potential of female bull trout in a river-reservoir system

The likelihood that fish will initiate spawning, spawn successfully, or skip spawning in a given year is conditioned in part on availability of energy reserves. We evaluated the consequences of spatial heterogeneity in thermal conditions on the energy accumulation and spawning potential of migratory bull trout ( Salvelinus confluentus ) in a regulated river–reservoir system. Based on existing data, we identified a portfolio of thermal exposures and migratory patterns and then estimated their influence on energy reserves of female bull trout with a bioenergetics model. Spawning by females was assumed to be possible if postspawning energy reserves equaled or exceeded 4 kJ/g. Given this assumption, results suggested up to 70% of the simulated fish could spawn each year. Fish that moved seasonally between a cold river segment and a warmer reservoir downstream had a greater growth rate and higher propensity to spawn in a given year (range: 40%–70%) compared with fish that resided solely in the cold river segment (25%–40%). On average, fish that spawned lost 30% of their energy content relative to their prespawn energy. In contrast, fish that skipped spawning accumulated, on average, 16% energy gains that could be used toward future gamete production. Skipped spawning occurred when water temperatures were relatively low or high, and if upstream migration occurred relatively late (mid-July or later) or early (early-May or earlier). Overall, our modeling effort suggests the configuration of thermal exposures, and the ability of bull trout to exploit this spatially and temporally variable thermal conditions can strongly influence energy reserves and likelihood of successful spawning.

Idaho↗
USGS2020

Beyond sticks and stones: Integrating physical and ecological conditions into watershed restoration assessments using a food web modeling approach

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.

Washington↗
USGS2020

Can nutrient additions facilitate recovery of Pacific salmon?

Multiple restoration actions have been implemented in response to declining salmon populations. Among these is the addition of salmon carcasses or artificial nutrients to mimic marine-derived nutrients historically provided by large spawning runs of salmon. A key assumption in this approach is that increased nutrients will catalyze salmon population growth. Although effects on aquatic ecosystems have been observed during treatments, it is unclear whether permanent population increases for salmon will occur. To test this assumption and address associated uncertainties, we linked a food web model with a salmon life cycle model to examine whether carcass additions in a river reach would improve conditions for salmon in the long term. Model results confirmed immediate increases in the biomass of periphyton, macroinvertebrates, and fish during carcass additions. In turn, juvenile salmon grew larger and experienced improved freshwater and smolt survival, which translated to a greater number of adults returning to spawn. However, once additions ceased, salmon abundance returned to pretreatment levels, which, based on our model, is owing to a combination of instream and out-of-basin factors. Overall, results of this work suggest that benefits during carcass and nutrient additions may not translate into persistent productivity of salmon unless additions are sustained indefinitely or other limiting factors are addressed.

Alberta, British Columbia, Idaho, Montana, Nevada,↗
USGS2019

Decision analysis for the reintroduction of Bull Trout into the lower Pend Oreille River, Washington

The decision to reintroduce a species can be difficult owing to conflicting opinions and objectives, as well as uncertainty of the outcome. Structured decision making addresses these considerations by identifying realistic fundamental objectives and building achievable management alternatives, within a quantitative modeling framework. The process is driven by participation of stakeholders that represent diverse objectives, policy mandates, and opinions regarding decision alternatives. We applied structured decision making to evaluate reintroduction of Bull Trout Salvelinus confluentus in the lower Pend Oreille River in northeastern Washington State. We engaged stakeholders from Tribal, municipal, county, state and federal agencies to specify fundamental objectives, formulate feasible reintroduction decisions, and conceptualize a modeling framework that includes biological information and stakeholder assumptions. Stakeholders requested iterative decision sets to determine the optimal recipient streams and release strategies. The optimal decision, based on the fundamental objective of maximizing adult abundance at year 10, was artificial propagation of 4500 juvenile Bull Trout coupled with translocation of 25 adult migrants to be reintroduced into a tributary and lake system that produced at least 18% more adult fish relative to alternatives. Sensitivity analyses were robust to the identity of the recipient stream (i.e., Sullivan Lake/Harvey Creek was always the optimal recipient stream) but suggested that maximizing the number of artificially produced juveniles released could produce a similar number of adult Bull Trout as the coupled release strategy. Results also suggested that ensuring fish passage at the Albeni Falls Dam in the mainstem Pend Oreille River could increase the abundance of adult fish. The process followed for this case study can be adapted to similar decisions regarding reintroduction or other translocations of fish in other systems.

Washington↗
USGS2018

Stream metabolism increases with drainage area and peaks asynchronously across a stream network

Quantifying the spatial and temporal dynamics of stream metabolism across stream networks is key to understanding carbon cycling and stream food web ecology. To better understand intra-annual temporal patterns of gross primary production (GPP) and ecosystem respiration (ER) and their variability across space, we continuously measured dissolved oxygen and modeled stream metabolism for an entire year at ten sites across a temperate river network in Washington State, USA. We expected GPP and ER to increase with stream size and peak during summer and autumn months due to warmer temperatures and higher light availability. We found that GPP and ER increased with drainage area and that only four sites adhered to our expectations of summer peaks in GPP and autumn peaks in ER while the rest either peaked in winter, spring or remained relatively constant. Our results suggest the spatial arrangement and temporal patterns of discharge, temperature, light and nutrients within watersheds may result in asynchronies in GPP and ER, despite similar regional climatic conditions. These findings shed light on how temporal dynamics of stream metabolism can shift across a river network, which likely influence the dynamics of carbon cycling and stream food webs at larger scales.

Washington↗