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Jason Dunham

Publications and source records attributed to Jason Dunham.

At least 19 recordsLinked to original sources
USGS2026

RoadxStr user’s guide—For collection of road-stream crossing assessment field observations

Intersections of drainage networks and road networks represent a critical nexus between natural waterways and human infrastructure. Managing these systems involves decisions related to management of infrastructure, hydrologic and geomorphic processes, and ecological connectivity. Interactions among these systems influence multiple values, including the intactness of transportation networks, public safety, water quality, and ecosystem function that collectively amount to billions of dollars. Despite the importance of road-stream crossings, there are countless gaps in knowing where and what they are. These gaps limit the degree to which managers can inventory and assess stream and road networks to inform decisions. To address this first-level need, we developed RoadxStr (road-stream crossings): a survey tool that effectively characterizes road-stream crossings across the full stream and drainage network. This document describes the RoadxStr Field Form, available within a mobile application, which is designed for rapid and standardized data collection involving assessment of a road-stream crossing, including the road, crossing structure(s), and the nearby hydrologic channel. This document provides instructions on how to (1) access and download the RoadxStr Field Form within the mobile application service and (2) use and complete a RoadxStr Field Form survey.

Techniques and Methods↗
USGS2026

Environment, taxonomy, and socioeconomics predict non-imperilment in freshwater fishes

Freshwater fishes are among the most threatened taxa, yet conservation assessments remain incomplete for many species. Freshwater fishes provide essential ecosystem services such as food security, recreational opportunities, and cultural significance. Despite heavy alterations to freshwater ecosystems, the reasons for species’ sensitivity and resistance to imperilment are unclear. To address this need, we develop a machine learning framework to predict global imperilment status for 10,631 freshwater fish species using a comprehensive set of environmental, socioeconomic, and intrinsic species-level predictors. Using updated IUCN Red List data, we train and validate Random Forest classifiers to distinguish imperiled (Vulnerable, Endangered, Critically Endangered) from non-imperiled species. We examine the relative influence of 52 variables derived from 12 global sources describing extrinsic environmental and socioeconomic factors and intrinsic species-specific characteristics. Our models achieve higher accuracy for non-imperiled species (90.1%) compared to imperiled species (81.8%), reflecting the greater heterogeneity of threats and conditions driving imperilment. Across models, key predictors include habitat variables, taxonomic order, hydrological characteristics, and disturbance indicators, underscoring the interplay between ecology, geography, and human pressures. This integrative, reproducible approach demonstrates the utility of machine learning for guiding proactive conservation and provides a scalable framework for global biodiversity risk assessment.

Nature Communications↗
USGS2025

Aridity reduces lag times between aquatic and terrestrial dry-down among watersheds and across years in the northwest US

Landscapes encompass both aquatic and terrestrial ecosystems that experience the same climate but may respond to climate in divergent ways. For example, the time lag between seasonal dry-down of terrestrial soil moisture and decline in streamflow has important implications for species and ecosystem processes across the aquatic–terrestrial interface. How these lags between aquatic and terrestrial hydrology vary with climate and spatial location within watersheds remains largely unexplored. Here, we examine seasonal patterns of aquatic–terrestrial dry-down across seven watersheds in the northwestern USA, spanning a wide range of aridity. We compared daily streamflow data from USGS gages at watershed outlets with simulated daily soil moisture (1979–2020) from multiple locations within each watershed. In all watersheds, annual dry cycles progressed sequentially through the following features: evapotranspiration, precipitation, shallow soil moisture, deep soil moisture, and finally streamflow. Seasonal streamflow minima lagged behind soil moisture minima for shorter durations in more arid watersheds and drier years. Within watersheds, lag times varied spatially due to interactions between elevation and aridity, with short lags in low-elevation soils near streams in arid watersheds and longer lags in less arid watersheds. Collectively, these results indicate shorter lags between seasonal aquatic and terrestrial dry periods in drier watersheds and years, and show that these tighter linkages are spatially aggregated in drier watersheds. The co-occurrence of seasonally dry conditions in both aquatic and terrestrial systems under increasing aridification is likely to intensify stressors on ecosystems and services. Recognizing these patterns may be critical for predicting ecosystem vulnerabilities and informing adaptation strategies to mitigate the impacts of seasonally dry conditions.

Montana, Oregon, Wyoming↗
USGS2025

RAD (Resist-Accept-Direct) switch points and triggers for adaptation planning

Climate change is transforming ecosystems globally. The Resist-Accept-Direct (RAD) framework has gained traction within many natural resource management institutions to help consider the decision space in response to this transformation. Because RAD helps manage for directional change, RAD choices entail considering which RAD pathway to implement and for how long. For example, one may accept a slowly changing ecosystem, but at a certain point, decide to begin resisting or directing the change an ecosystem is experiencing. Alternatively, one may begin resisting an ecosystem transformation, but ultimately realize resistance is no longer feasible based on cost or efficacy. These choices are challenging and encompass broad domains of cultural, ecological, financial, organizational, public, regulatory, and technological considerations to determine when to switch RAD pathways. We introduce the concepts of RAD switch points and triggers to help support these decision processes. We illustrate these concepts using case studies on walleye ( Sander vitreus ) stocking decisions in Wisconsin, wildfire response in the Greater Yellowstone Ecosystem, and bull trout ( Salvelinus confluentus ) management in Oregon, USA. Synthesizing across these examples, we delineate key points for decision makers as they (iteratively) reevaluate among the RAD pathways as conditions continue to change.

Journal of Environmental Management↗
USGS2025

A streamflow permanence classification model for forested streams that explicitly accounts for uncertainty and extrapolation

Accurate mapping of headwater streams and their flow status has important implications for understanding and managing water resources and land uses. However, accurate information is rare, especially in rugged, forested terrain. We developed a streamflow permanence classification model for forested lands in western Oregon using the latest light detection and ranging-derived hydrography published in the National Hydrography Dataset. Models were trained using 2,518 flow/no flow field observations collected in late summer 2019–2021 across headwaters of 129 sub-watersheds. The final model, the Western Oregon WeT DRy model, used Random Forest and 13 environmental covariates for classifying every 5-m stream sub-reach across 426 sub-watersheds. The most important covariates were annual precipitation and drainage area. Model output included probabilities of late summer surface flow presence and were subsequently categorized into three streamflow permanence classes—Wet, Dry, and Ambiguous. Ambiguous denoted model probabilities and associated prediction intervals that extended over the 50% classification threshold between wet and dry. Model accuracy was 0.83 for sub-watersheds that contained training data and decreased to 0.67 for sub-watersheds that did not have observations of late summer surface flow. The model identified where predictions extrapolated beyond the domain characterized by the training data. The combination of spatially continuous estimates of late summer streamflow status along with uncertainty and extrapolation estimates provide critical information for strategic project planning and designing additional field data collection.

Oregon↗
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

Population genomics reveals local adaptation related to temperature variation in two stream frog species: Implications for vulnerability to climate warming

Identifying populations at highest risk from climate change is a critical component of conservation efforts. However, vulnerability assessments are usually applied at the species level, even though intraspecific variation in exposure, sensitivity and adaptive capacity play a crucial role in determining vulnerability. Genomic data can inform intraspecific vulnerability by identifying signatures of local adaptation that reflect population-level variation in sensitivity and adaptive capacity. Here, we address the question of local adaptation to temperature and the genetic basis of thermal tolerance in two stream frogs ( Ascaphus truei and A. montanus ). Building on previous physiological and temperature data, we used whole-genome resequencing of tadpoles from four sites spanning temperature gradients in each species to test for signatures of local adaptation. To support these analyses, we developed the first annotated reference genome for A. truei . We then expanded the geographic scope of our analysis using targeted capture at an additional 11 sites per species. We found evidence of local adaptation to temperature based on physiological and genomic data in A. montanus and genomic data in A. truei , suggesting similar levels of sensitivity (i.e., susceptibility) among populations regardless of stream temperature. However, invariant thermal tolerances across temperatures in A. truei suggest that populations occupying warmer streams may be most sensitive. We identified high levels of evolutionary potential in both species based on genomic and physiological data. While further integration of these data is needed to comprehensively evaluate spatial variation in vulnerability, this work illustrates the value of genomics in identifying spatial patterns of climate change vulnerability.

Idaho, Montana, Oregon, Washington↗
USGS2025

Exposure, sensitivity, or adaptive capacity? Reviewing assessments that use only two of three elements of climate change vulnerability

As climate change accelerates, understanding which species are most vulnerable and why they are vulnerable will be vital to inform conservation action. Climate change vulnerability assessments (CCVAs) are tools to assess species' responses to climate change, detect drivers of vulnerability, and inform conservation planning. CCVAs are commonly composed of three elements: exposure, sensitivity, and adaptive capacity. Incorporating all three elements can be challenging, and including only two of the three elements may be a more feasible approach in many systems. Although two-element CCVA approaches have become more common, their utility and procedures remain poorly documented. We conducted a literature review to explore the scope, methods, and rationale of CCVAs that use a two-element approach to assess vertebrate vulnerability. Despite the potential to expand CCVAs into understudied systems, two-element assessments had similar geographic and taxonomic biases as those previously detected in CCVAs in general. Methods varied, yet we found that variables used in two-element studies could be condensed into standardized categories to enhance comparability. Finally, limitations in data availability and computational resources were common rationales for using a two-element approach. By clarifying the purposes, opportunities, and limitations of two-element assessment, this review can aid in selecting appropriate methods for CCVAs.

Conservation Science and Practice↗
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

Greater plasticity in CTmax with increased climate variability among populations of tailed frogs

Temporally variable climates are expected to drive the evolution of thermal physiological traits that enable performance across a wider range of temperatures (i.e. climate variability hypothesis, CVH). Spatial thermal variability, however, may mediate this relationship by providing ectotherms with the opportunity to behaviourally select preferred temperatures (i.e. the Bogert effect). These antagonistic forces on thermal physiological traits may explain the mixed support for the CVH within species despite strong support among species at larger geographical scales. Here, we test the CVH as it relates to plasticity in physiological upper thermal limits (critical thermal maximum—CTmax) among populations of coastal tailed frogs ( Ascaphus truei ). We targeted populations that inhabit spatially homogeneous environments, reducing the potentially confounding effects of behavioural thermoregulation. We found that populations experiencing greater temporal thermal variability exhibited greater plasticity in CTmax, supporting the CVH. Interestingly, we identified only one site with spatial temperature variability and tadpoles from this site demonstrated greater plasticity than expected, suggesting the opportunity for behavioural thermoregulation can reduce support for the CVH. Overall, our results demonstrate one role of climate variability in shaping thermal plasticity among populations and provide a baseline understanding of the impact of the CVH in spatially homogeneous thermal landscapes.

Proceedings of the Royal Society B↗
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

The past, present, and a future for native charr in Japan

Charrs ( Salvelinus ) reach their southernmost distribution in Japan, and are uniquely adapted to the short, steep streams of this island archipelago. Southern Asian Dolly Varden ( Salvelinus curilus ) occur only in Hokkaido Island, whereas white-spotted charr ( Salvelinus leucomaenis ) range to southern Honshu. Both species diverged from an ancestral lineage during the late Pliocene/early Pleistocene, when lowered sea levels created semi-enclosed water bodies in the seas of Japan and Okhotsk. Genetic analyses showed S. curilus represents the most ancient divergence from the Dolly Varden ( Salvelinus malma ) - Arctic charr ( Salvelinus alpinus ) group, and revealed five lineages of S. leucomaenis which align differently than traditional subspecies. Japanese charr display diverse and flexible life histories including anadromous fish with partial migration, and fluvial, adfluvial, and resident forms. In Hokkaido, Dolly Varden are distributed upstream and white-spotted charr downstream. They coexist in narrow sympatric zones through adaptive shifts by Dolly Varden in behavior and morphology that facilitate benthic foraging. Both species hybridize with native and nonnative salmonids, and are displaced from microhabitats and decline in abundance when rainbow trout ( Oncorhynchus mykiss ) and brown trout ( Salmo trutta ) invade. Japan streams contain over 95,000 erosion control dams which create short stream fragments (medians ~200 m). This has increased extirpation of charr populations via lower genetic diversity and stochastic and demographic factors. Tributaries provide complex rearing habitats, afford refuges from floods, and supply recruits that sustain populations in mainstem fragments and create metapopulations in connected riverscapes. Charr play central roles in linked stream-riparian food webs, and cause direct and indirect effects that cascade to streambed algae and riparian predators when linkages are disrupted by anthropogenic effects or altered by native parasites. Many charr populations are threatened by habitat fragmentation and introgression or invasion by nonnative forms, but efforts to conserve charr are growing. These include restoring connectivity among pure populations above barriers that prevent invasions, protecting tributary nurseries, and instituting angling regulations to protect headwater populations. Key steps include inventorying pure populations, identifying conservation units, selecting appropriate management based on connectivity and biotic interactions, and engaging stakeholders and youth to engender an ethic for conserving irreplaceable charr lineages.

Ichthyological Research↗
USGS2024

Effects of culverts on habitat connectivity in streams—A science synthesis to inform National Environmental Policy Act analyses

The U.S. Geological Survey is working with Federal land management agencies to develop a series of science syntheses to support environmental effects analyses that agencies conduct to comply with the National Environmental Policy Act (NEPA). This report synthesizes science information about the potential effects of culverts on stream connectivity and subsequent effects on fish. We conducted a structured search of published scientific literature to find information about (1) culvert design, installation, and degradation; (2) methods for analyzing culvert condition and quantifying stream connectivity; and (3) the effects of changes to stream connectivity on freshwater fish. We follow the organization first established in U.S. Geological Survey Scientific Investigations Report 2023-5114, in which the report sections align with standard elements of NEPA analyses. We found that, while the effects of dams on stream biota are well documented, smaller barriers at road crossings, like culverts, are prevalent and collectively have a substantial effect on habitat connectivity. Individual culverts differ in the degree to which they impede the movement of aquatic organisms, and we documented methods to assess and estimate the permeability of a culvert, or the ability of aquatic organisms to pass through it. Finally, we outlined methods for using culvert location and permeability information to quantify connectivity in a watershed based on the Dendritic Connectivity Index. Studies have shown that channel constriction, perched outlets, and extreme flow velocities are some of the characteristics of culverts that may hinder aquatic organism passage. Culverts can serve as daily and seasonal barriers to fish, disrupting access to habitat and essential resources like cold water or overwintering refuges. Reduced connectivity can have population-level effects, leading to lower fish species richness and abundance in affected watersheds. Public land managers can use this report by incorporating it by reference in NEPA documentation, as supplemental information, or as a general reference for literature about the effects of culverts on stream connectivity and freshwater fish.

Scientific Investigations Report↗
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↗
USGS2024

Coldwater fish in wadeable streams

Although we are consistent with the past edition of this volume regarding standard sampling techniques for wadeable, coldwater streams, this edition reflects recent literature, advances in calibrating numbers, and obtaining lengths of fish collected and provides additional clarity regarding effort. We also specify a minimum of two netters and one electrofisher operator for backpack electrofishing to allow capture of fish that “roll” downstream without surfacing (e.g., fish like sculpins, which lack swim bladders); however, as in the past edition, a minimum of one netter and one operator may be used on studies focused on fish with swim bladders, like salmonids (salmons and trouts). Finally, this chapter mentions specifically what factors should lead to standard adjustments to techniques to account for the range of habitat features typically encountered in headwater streams. Small, wadeable streams comprise most habitats available to fish in fluvial networks. Wadeable streams are generally less than 1 m deep, and fish can be sampled without the use of float craft. Cold waters are generally defined as having mean 7-d summer maximum water temperatures less than 20°C, providing habitat for coldwater fishes. Fish fauna of small, coldwater North American streams typically include salmonids, sculpins, minnows, sticklebacks, suckers, or lampreys (Hocutt and Wiley 1986). Standard sampling protocols provided herein apply most readily to salmonids because of their sport and commercial values (Johnson et al. 2007). Salmonids also have cultural values, are well studied and widely distributed, and act as predators, competitors, and prey (Lee et al. 1997). However, many of these methods can also be applied effectively to sample nonsalmonids. As interest in nonsalmonid species grows, further development and investigation of sampling methods for a broader diversity of species is expected (see section 8.5).

Book chapter↗