Assistant Unit Leader - Alaska Fish and Wildlife Cooperative Research Unit
Jeff earned his BS in Biology and Chemistry from Northern Arizona University and his MS and PhD in Ecology from the University of North Carolina at Chapel Hill. He has been involved in basic and applied research in a variety of river ecosystems worldwide, including dam removal in Fossil Creek, Arizona, wetland mitigation in North Carolina, food web studies on the Danube River in Austria/Hungary/Serbia and glacially-fed rivers in Italy, and large dam impacts on the Colorado River.
His current role at USGS is at the Alaska Cooperative Fisheries and Wildlife Research Unit as an Assistant Unit Leader in Fisheries, in cooperation with the University of Alaska Fairbanks and partners. Jeff is a river and stream ecologist who specializes in macroinvertebrate communities, fisheries, and food webs. His research is focused on linking hydrological and geomorphic conditions in rivers to the structure of aquatic communities.
Science and Products
Little bugs, big data, and Colorado River adaptive management: Preliminary findings from the ongoing bug flow experiment at Glen Canyon Dam
Experimental reductions in sub-daily flow fluctuations increased gross primary productivity for 425 river kilometers downstream
Applied citizen science in freshwater research
Hydropeaking intensity and dam proximity limit aquatic invertebrate diversity in the Colorado River Basin
Variables affecting resource subsidies from streams and rivers to land and their susceptibility to global change stressors
Net-spinning caddisfly distribution in large regulated rivers
Spatial population structure of a widespread aquatic insect in the Colorado River Basin: Evidence for a Hydropsyche oslari species complex
Bug flows: Don’t count your midges until they hatch
Aquatic–terrestrial linkages provide novel opportunities for freshwater ecologists to engage stakeholders and inform riparian management
Deleterious effects of net clogging on the quantification of stream drift
Phenology of the adult angel lichen moth (Cisthene angelus) in Grand Canyon, USA
Incorporating temporal heterogeneity in environmental conditions into a somatic growth model
Non-USGS Publications**
**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
Community Science Light Trapping in Grand Canyon
Invertebrate Drift Downstream of Colorado River Basin Dams
Understanding Factors Influencing Rainbow Trout Growth in the Colorado River
Insect Drift
Aquatic Insects
Gross primary production estimates and associated light, sediment, and water quality data from the Colorado River below Glen Canyon Dam
Population genetic analysis of three aquatic macroinvertebrate species from samples in Grand Canyon (Arizona, USA) tributaries and nearby reference streams, 2016-2021
Benthic macroinvertebrate tailwater data in the Colorado River Basin, 2013 & 2015
Carbon, nitrogen, and phosphorus content of adult emergent Diptera before and after a fire-storm sequence in the Colorado River near Shinumo Creek, Grand Canyon, AZ
Stream Drift Sampling in Arizona, 2014Data
Angel Lichen Moth Abundance and Morphology Data, Grand Canyon, AZ, 2012
Flow management for hydropower extirpates aquatic insects, undermining river food websData
Science and Products
- Publications
Filter Total Items: 17
Little bugs, big data, and Colorado River adaptive management: Preliminary findings from the ongoing bug flow experiment at Glen Canyon Dam
The undammed Colorado River in Grand Canyon was characterized by spring snow-melt floods that sometimes exceeded 100,000 cubic feet per second (cfs). These were followed by occasional flash floods during summer monsoons, then by low flows from fall through early spring (Figure 1; Topping and others, 2003). This seasonally variable flow regime carried huge loads of sediment and was an important driExperimental reductions in sub-daily flow fluctuations increased gross primary productivity for 425 river kilometers downstream
Aquatic primary production is the foundation of many river food webs. Dams change the physical template of rivers, often driving food webs toward greater reliance on aquatic primary production. Nonetheless, the effects of regulated flow regimes on primary production are poorly understood. Load following is a common dam flow management strategy that involves sub-daily changes in water releases propApplied citizen science in freshwater research
Worldwide, scientists are increasingly collaborating with the general public. Citizen science methods are readily applicable to freshwater research, monitoring, and education. In addition to providing cost-effective data on spatial and temporal scales that are otherwise unattainable, citizen science provides unique opportunities for engagement with local communities and stakeholders in resource maHydropeaking intensity and dam proximity limit aquatic invertebrate diversity in the Colorado River Basin
River biodiversity is threatened globally by hydropower dams, and there is a need to understand how dam management favors certain species while filtering out others. We examined aquatic invertebrate communities within the tailwaters 0–24 km downstream of seven large hydropower dams in the Colorado River Basin of the western United States. We quantified aquatic invertebrate dominance, richness, abuVariables affecting resource subsidies from streams and rivers to land and their susceptibility to global change stressors
Stream and river ecosystems provide subsidies of emergent adult aquatic insects and other resources to terrestrial food webs, and this lotic–land subsidy has garnered much attention in recent research. Here, we critically examine a list of biotic and abiotic variables—including productivity, dominant taxa, geomorphology, and weather—that should be important in affecting the nature of these subsidyNet-spinning caddisfly distribution in large regulated rivers
Most of the world's large rivers are dammed for the purposes of water storage, flood control, and power production. Damming rivers fundamentally alters water temperature and flows in tailwater ecosystems, which in turn affects the presence and abundance of downstream biota.We collaborated with more than 200 citizen scientists to collect 2,194 light trap samples across 2 years and more than 2,000 rSpatial population structure of a widespread aquatic insect in the Colorado River Basin: Evidence for a Hydropsyche oslari species complex
Structural connectivity and dispersal ability are important constraints on functional connectivity among populations. For aquatic organisms that disperse among stream corridors, the regional structure of a river network can, thus, define the boundaries of gene flow. In this study, we used mitochondrial DNA (mtCO1 barcoding gene) to examine the genetic diversity and population structure of a caddisBug flows: Don’t count your midges until they hatch
Usually when people hear about a “bug problem” it’s due to an undesirable overabundance of insects (think plague of locusts). In the Colorado River in Grand Canyon, however, we are faced with the opposite predicament: the river is essentially devoid of bugs. Aquatic insects are a fundamental component of a healthy river ecosystem. Most aquatic insects spend their juvenile life stages (egg, larva,Aquatic–terrestrial linkages provide novel opportunities for freshwater ecologists to engage stakeholders and inform riparian management
Studies of aquatic–terrestrial ecosystem linkages explore the mechanisms by which components of one ecosystem, such as the aquatic insect community in a stream, directly affect components of an adjacent ecosystem, such as the density and diversity of riparian predators. On a human level, research into these linkages allows freshwater ecologists to form novel collaborations with stakeholders and otDeleterious effects of net clogging on the quantification of stream drift
Drift studies are central to stream and river ecological research. However, a fundamental aspect of quantifying drift — how net clogging affects the accuracy of results — has been widely ignored. Utilizing approaches from plankton and suspended sediment studies in oceanography and hydrology, we examined the rate and dynamics of net clogging across a range of conditions. We found that nets clog nonPhenology of the adult angel lichen moth (Cisthene angelus) in Grand Canyon, USA
We investigated the phenology of adult angel lichen moths (Cisthene angelus) along a 364-km long segment of the Colorado River in Grand Canyon, Arizona, USA, using a unique data set of 2,437 light-trap samples collected by citizen scientists. We found that adults of C. angelus were bivoltine from 2012 to 2014. We quantified plasticity in wing lengths and sex ratios among the two generations and acIncorporating temporal heterogeneity in environmental conditions into a somatic growth model
Evaluating environmental effects on fish growth can be challenging because environmental conditions may vary at relatively fine temporal scales compared to sampling occasions. Here we develop a Bayesian state-space growth model to evaluate effects of monthly environmental data on growth of fish that are observed less frequently (e.g., from mark-recapture data where time between captures can rangeNon-USGS Publications**
Clay, P.A., Muehlbauer, J.D., and Doyle, M.W., 2015, Effect of tributary and braided confluences on aquatic macroinvertebrate communities and geomorphology in an alpine river watershed: Freshwater Science, v. 34, no. 3, p. 845-856.Copp, A.J., Kennedy, T.A., and Muehlbauer, J.D., 2014, Barcodes are a useful tool for labeling and tracking ecological samples: Bulletin of the Ecological Society of America, v. 95, no. 3, p. 293–300.Muehlbauer, J.D., Collins, S.F., Doyle, M.W., and Tockner, K., 2014, How wide is a stream? Spatial extent of the potential “stream signature” in terrestrial food webs using meta-analysis: Ecology, v. 95, no. 1, p. 44–55.Wang, H., Li, H., Zhang, Z., Muehlbauer, J.D., He, Q., Xu, X., Yue, C., and Jiang, D., 2014, Linking stoichiometric homeostasis of microorganisms with soil phosphorus dynamics in wetlands subjected to microcosm warming: PLoS ONE, v. 9, no. 1, p. e85575.Riggsbee, J.A., Doyle, M.W., Julian, J.P., Manners, R., Muehlbauer, J.D., Sholtes, J.S., and Small, M.J., 2013, Influence of aquatic and semi-aquatic organisms on channel forms and processes, in Wohl, E., ed., Fluvial Geomorphology: San Diego, California, USA, Academic Press, p. 189-202.Muehlbauer, J.D., and Doyle, M.W., 2012, Knickpoint effects on macroinvertebrates, sediment, and discharge in urban and forested streams: urbanization outweighs microscale habitat heterogeneity: Freshwater Science, p. 282–295.Muehlbauer, J.D., Duncan, J.M., and Doyle, M.W., 2012, Benign use of salt slugs on aquatic macroinvertebrates: measuring discharge with salt during an aquatic ecology study: River Research and Applications, v. 28, no. 10, p. 1858-1863.Muehlbauer, J.D., Doyle, M.W., and Bernhardt, E.S., 2011, Macroinvertebrate community responses to a dewatering disturbance gradient in a restored stream: Hydrology and Earth System Sciences, v. 15, no. 6, p. 1771-1783.Fuller, R.L., Griego, C., Muehlbauer, J.D., Dennison, J., and Doyle, M.W., 2010, Response of stream macroinvertebrates in flow refugia and high-scour areas to a series of floods: a reciprocal replacement study: Journal of the North American Benthological Society, v. 29, no. 2, p. 750-760.Muehlbauer, J.D., LeRoy, C.J., Lovett, J.M., Flaccus, K.K., Vlieg, J.K., and Marks, J.C., 2009, Short-term responses of decomposers to flow restoration in Fossil Creek, Arizona, USA: Hydrobiologia, v. 618, p. 35-45.Joseph, J.W., Odegaard, M.L., Ronnebaum, S.M., Burgess, S.C., Muehlbauer, J., Sherry, A.D., and Newgard, C.B., 2007, Normal flux through ATP-citrate lyase or fatty acid synthase is not required for glucose-stimulated insulin secretion: Journal of Biological Chemistry, v. 282, no. 43, p. 31592-31600.**Disclaimer: The views expressed in Non-USGS publications are those of the author and do not represent the views of the USGS, Department of the Interior, or the U.S. Government.
- Science
Community Science Light Trapping in Grand Canyon
Aquatic insects are commonly used to gauge the health of stream and river ecosystems, yet collecting enough samples to adequately characterize a river segment as long as the Colorado River through Grand Canyon (> 250 miles) would be essentially impossible using traditional sampling methods. Since 2012, our group has been collaborating with river guides, private boaters, and educational groups to...Invertebrate Drift Downstream of Colorado River Basin Dams
Aquatic invertebrates are critical food for fish and other species that inhabit large rivers. In the Colorado River Basin, invertebrates that get transported down the river (“in the drift”) are particularly important to rainbow trout and other species of interest to recreational users. This research seeks to compare rivers downstream of large dams throughout the Colorado River Basin in order to...Understanding Factors Influencing Rainbow Trout Growth in the Colorado River
Rainbow trout is a desirable sport fish that has been introduced in many locations around the world. Although introductions of rainbow trout and other nonnative fishes provide recreational fishing opportunities, they also pose threats to native fish populations. The Glen Canyon Dam Adaptive Management Program has tasked scientists and managers with identifying management options that allow rainbow...Insect Drift
All aquatic invertebrates drift downstream at some point in their life cycle. Invertebrates may drift to find more preferable habitats, to leave the water during their transition from aquatic larvae to terrestrial adults, or accidentally such as when swept off the river bed by a flood. Regardless, when they enter the drift, invertebrates become particularly susceptible to predation by several...Aquatic Insects
Aquatic insects live in the water as larvae most of their lives, then emerge onto land for a brief period as winged adults. Sampling these emerged adults on land is therefore a useful tool for understanding the condition of the aquatic insect population that is in the water, particularly in large rivers where sampling the larvae on the river bed is impractical. Our group uses a variety of methods... - Data
Gross primary production estimates and associated light, sediment, and water quality data from the Colorado River below Glen Canyon Dam
These data were compiled to model the effects of flow regime and bed grain size distributions on rates of gross primary production (GPP) in the Colorado River below Glen Canyon Dam, AZ, USA. The objectives of our study were to quantify daily and weekly scale effects of an experimental flow regime on GPP in the Colorado River. The experimental flow was conducted at Glen Canyon Dam from May-August iPopulation genetic analysis of three aquatic macroinvertebrate species from samples in Grand Canyon (Arizona, USA) tributaries and nearby reference streams, 2016-2021
This dataset contains single nucleotide polymorphism (SNP) information for aquatic insect species collected in tributaries of the Colorado River in Grand Canyon (Arizona, USA), as well as SNP information for individuals collected from reference reaches of the Upper Colorado River Basin in Utah. This dataset focuses specifically on three species that were common and widely distributed throughout trBenthic macroinvertebrate tailwater data in the Colorado River Basin, 2013 & 2015
These benthic macroinvertebrate data and associated site characteristics were compiled for the purpose of exploring any relationships between large dams in the Colorado River Basin, their flow management and geographical context, and their associated downstream benthic macroinvertebrate communities. The goal of the analyses based upon these data was to understand how dam conditions, specifically hCarbon, nitrogen, and phosphorus content of adult emergent Diptera before and after a fire-storm sequence in the Colorado River near Shinumo Creek, Grand Canyon, AZ
This dataset includes total phosphorus (TP), total nitrogen (TN), and total carbon (TC) concentrations as well as δ15N and δ13C composition, and overall C:N:P stoichiometry for adult emergent Diptera from the Colorado River, Grand Canyon, AZ. The samples were collected before and after a fire and subsequent storm occurred in the Shinumo Watershed, a tributary to the ColStream Drift Sampling in Arizona, 2014Data
These data were compiled from field drift collections and from a meta-analysis of published drift literature. Field data were collected in 2014 from the Colorado River downstream of Glen Canyon Dam, Arizona, from the Salt River downstream of Stewart Mountain Dam, Arizona, and from Wet Beaver Creek near the Village of Oak Creek, Arizona. These data represent flow meter measurements taken at the mouAngel Lichen Moth Abundance and Morphology Data, Grand Canyon, AZ, 2012
Two unique datasets on the abundance and morphology of the angel lichen moth (Cisthene angelus) in Grand Canyon, Arizona, USA were compiled to describe the phenology and life history of this common, but poorly known, species. The abundance data were collected from 2012 to 2013 through a collaboration with river runners in Grand Canyon National Park. These citizen scientists deployed light traps frFlow management for hydropower extirpates aquatic insects, undermining river food websData
Two unique datasets were gathered to document whether flow management for hydropower affects the abundance and diversity of aquatic insect assemblages. The first dataset was collected in Grand Canyon from 2012-2014 by citizen scientists rafting the Colorado River. Simple light traps were set out each night in camp and used to capture the adult life stages of aquatic insects that emerged from the C - News