Phaedra Budy’s research while affiliated with Utah State University and other places

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Publications (189)


Establishing a baseline to assess impact of restoration actions reconnecting Bear Lake tributaries to increase resilience and abundance of native fishes
  • Technical Report
  • Full-text available

November 2024

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21 Reads

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James Derito

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Phaedra Budy
Download


Map of the Henrys Fork watershed with sampling locations and an abstracted example reach showing our sampling structure. The inset map shows geographical context in the United States, in North America. Reaches are labeled in order of annual average submerged macrophyte coverage, from lowest (1) to highest (5). Each reach was sampled up to three times: spring, summer, and fall
True-color aerial imagery (top image) and false-color digital elevation model (DEM, bottom image) showing bathymetry for reach 4 on the Henrys Fork. Inset map shows larger spatial context in the U.S. state of Idaho. We labeled random habitat sampling locations with white numbers representing the habitat types identified through k-means cluster analysis. Images were collected in August 2020, and random habitat sampling to identify habitat types occurred in October 2020. Sampling locations in the reach are labeled to 2 m accuracy
Proportion of k-means clustering analysis-defined physical habitat types across all reach-scale macrophyte coverage values
Top panel shows Net Rate of Energy Intake (NREI) at each sampling point within each reach grouped by habitat type across reach-averaged submerged macrophyte coverage. Bottom panel shows elected habitat frequency across reach-averaged submerged macrophyte coverage. Elected habitat frequency describes the frequency of preferred habitat types for trout within a reach, while NREI represents potential trout growth and productivity within habitat types and across reach-scale submerged macrophyte coverage
Violin plot showing NREI within each habitat type across all 390 random habitat samples. Colors represent habitat types. White dot is median, black bar is interquartile range, whiskers represent 1.5 times the interquartile range. The colored area represents a kernel density estimation to show the distribution shape of the data; wider sections represent a higher probability that members of the population take on that value, while skinnier sections represent a lower probability

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The reach-scale biogeomorphic effect of submerged macrophytes on trout habitat suitability

Hydrobiologia

Submerged macrophytes have complex effects on spatiotemporal characteristics of river ecosystems, including trout habitat. We investigated the impact of submerged macrophyte coverage on trout habitat in the Henrys Fork of the Snake River, Idaho, USA. We hypothesized that higher submerged macrophyte coverage would create new habitat types beneficial for trout growth. We assessed river physical and biotic attributes, trout habitat preferences, and estimated trout growth potential with bioenergetics models across a gradient of submerged macrophyte coverage (32–94%). We identified four distinct habitat types within the riverscape shaped by submerged macrophyte coverage. Increased submerged macrophyte coverage increased the frequency of habitat types with higher trout growth potential but reduced the occurrence of preferred habitat types. We observed no relationship between reach-scale trout growth potential and submerged macrophyte coverage. However, an outlier of very high trout growth potential at 94% submerged macrophyte coverage suggests a potential threshold effect. More study is required but our observations suggest macrophyte growth homogenized physical habitat characteristics, reduced flow velocities, and increased invertebrate drift, thereby enhancing trout growth potential. Our findings underscore the complex interplay between submerged macrophytes and trout habitat dynamics across scales, emphasizing the importance of considering both physical and biological effects on trout habitat.


Movement patterns of a small-bodied minnow suggest nomadism in a fragmented, desert river

July 2024

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129 Reads

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1 Citation

Movement Ecology

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Phaedra Budy

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Background Unfettered movement among habitats is crucial for fish to access patchily distributed resources and complete their life cycle, but many riverscapes in the American Southwest are fragmented by dams and dewatering. The endangered Rio Grande silvery minnow (Hybognathus amarus, RGSM) persists in a fragmented remnant of its former range (ca. 5%), and its movement ecology is understudied. Methods We tracked movements of hatchery-reared RGSM, tagged with passive integrated transponder tags, using stationary and mobile antennas from 2019 to 2022. We quantified probability of movement and total distance moved by RGSM released above and below a dam. We then assessed how well two prevailing riverine movement theories (i.e., restricted movement paradigm [RMP] and colonization cycle hypothesis [CCH]) explained RGSM movement patterns. Results We detected 36.8% of released RGSM (n = 37,215) making at least one movement. Movements were leptokurtic and substantially greater than expected based on the RMP for both stationary (1.7–5.9 m) and mobile (30.3–77.8 m) individuals. On average, RGSM were detected at large for 75 days and moved a total of 12.2 rkm within a year. The maximum total distance moved by RGSM was 103 rkm. Similarly, we observed a multimodal distribution of detected range sizes with a mean detected range of 2.4 rkm and a maximum detected range of 78.2 rkm. We found little support for an upstream movement bias, as expected under the CCH, and most movements (74%) were directed downstream. Conclusions Our data suggest RGSM are highly mobile, with the ability to make long-distance movements. Neither movement theory adequately described movement patterns of RGSM; instead, our findings support a nomadic movement pattern and an apparent drift paradox matching recent studies of other pelagic-broadcast spawning minnows where populations persist upstream despite experiencing downstream drift as larvae. Resolution of the drift paradox may be achieved through further, targeted studies into different aspects of the species’ life history. Quantification of RGSM movement provides crucial insights into the species’ movement ecology and may help define the appropriate scale of recovery efforts.


Wood you believe it? Experimental addition of nonnative wood enhances instream habitat for native dryland fishes

June 2024

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65 Reads

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1 Citation

River Research and Applications

Flow alteration and riparian vegetation encroachment are causing habitat simplification with severe consequences for native fishes. To assess the effectiveness of enhancing simplified habitat in a large dryland river, we experimentally added invasive wood at 19 paired treatment and reference (no wood added) subreaches (50–100 m) within the main channel of the San Juan River. Using a before-after-control-impact design, we sampled fishes and macroinvertebrates, and quantified habitat complexity. After wood addition, total native fish densities were 2.2× higher in treatments compared with references, whereas total nonnative fish densities exhibited no response. Macroinvertebrate densities were 6.8× higher, and habitat complexity increased in treatments. Counts of geomorphic features in treatments increased from 1 to a maximum of 11 following wood addition, while the number of features in references remained unchanged. Wood addition has potential to instigate natural riverine processes, ultimately enhancing native fish habitat by increasing macroinvertebrate densities and habitat complexity in dryland rivers. Water overallocation and increasing aridity will continue to challenge efforts to improve habitat conditions with environmental flows alone, and managers might consider integrating non-flow alternatives like addition of abundant, invasive wood to reduce habitat simplification.


Establishing a baseline to assess the impact of restoration actions reconnecting a Bear Lake tributary

March 2024

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44 Reads

Establishing baseline conditions and post-restoration standardized monitoring is critical to assessing the impact of restoration. In preparation for a planned culvert removal to reconnect upstream migration for cutthroat trout in North Eden Creek, a tributary of Bear Lake, we are characterizing the current fish community and habitat conditions, and designing a monitoring plan capable of determining long-term success of restoration.


Beaver dam analogs did not improve beaver translocation outcomes in a desert river

February 2024

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95 Reads

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1 Citation

Restoration Ecology

Stream restoration programs employ beaver‐related restoration techniques, including beaver translocations and installation of beaver dam analogs (BDA), to create complex in‐stream habitat. We investigated whether BDA installations improved the probability of translocated beavers surviving and colonizing a section of a degraded desert river. We translocated beavers fitted with tracking devices to the Price River, Utah, United States, for 2 years before and after BDAs were installed. We monitored survival and site fidelity of beavers to estimate apparent survival ( φ ), using model selection to evaluate models with BDA, flow, and other factors hypothesized to relate to apparent survival. We found similar apparent survival 8 weeks post‐release of pre‐BDA ( φ = 0.50 ± 0.08 SE) and post‐BDA beavers ( φ = 0.41 ± 0.06 SE). There were 15 predator‐caused mortalities and 39 beavers emigrated out of the study site. Top models indicated apparent survival was negatively related to mean flow. Of the 70 BDAs constructed, beaver activity was detected on only two structures and the number of intact natural dams decreased due to monsoon floods. Our results suggest BDAs may not improve survival and site fidelity of translocated beavers in desert river systems. Instead, the dynamic flow of desert rivers and negative relationship between flow and apparent survival suggest the timing of release may be an important consideration for successful beaver translocation. Additional research is needed to understand how habitat, food availability, individual behavior, and resident conspecifics influence beaver translocation success.



Expansive, positive changes to fish habitat diversity following the formation of a valley plug in a degraded desert river

September 2023

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69 Reads

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1 Citation

River Research and Applications

Widespread hydrologic alterations have simplified in‐stream habitats in rivers globally, driving population declines and extirpations of many native fishes. Here, we examine how rapid geomorphic change in a historically degraded desert river has influenced habitat diversification and ecosystem persistence. In 2010, a large reach of the degraded and simplified lower San Rafael River (SRR), Utah, was impacted by the formation of a valley plug and began to shift from a homogenous, single‐thread channel to a complex, multi‐threaded riverscape. We combined field measurements and drone‐collected imagery to document changes in fish habitat due to the valley plug. Our results demonstrate that in 2021, the affected reach was more diverse than any other stream reach along the SRR, containing 641% more diverse habitat (e.g., pools, riffles, and backwaters) than what was measured in 2015. The plug reach also retained water for periods beyond what was expected during seasonal drying, with the total extent of inundation within the riverscape increasing by over 2800%. Since the formation of the valley plug, riparian habitat has increased by 230% and channel networks have expanded to more than 50 distinct channels throughout the zone of influence. Our results provide evidence of successful self‐restoration in a formerly highly degraded reach of desert river, and encourage new methods of desert river restoration. We aim to inform the use of large‐scale, disruptive restoration actions like intentional channel occlusions, with the goal of mitigating the impacts of simplification and increasing habitat persistence in the face of exacerbated aridity in the desert Southwest.


The scale-dependent role of submerged macrophytes as drift-feeding lotic fish habitat

June 2023

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64 Reads

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2 Citations

Although submerged macrophyte (hereafter, “macrophyte”) communities are globally prevalent in low-gradient rivers, the net reach-scale effect of macrophytes on drift-feeding fish microhabitat preference is poorly understood. We used snorkeling and bioenergetics to study fish habitat selection for rainbow trout (Oncorhynchus mykiss) in the Henrys Fork, ID, USA, investigating microhabitat preference across a reach-scale gradient of macrophyte growth. Fish preferred microhabitats with deep water, low velocity, and low macrophyte coverage. Preferences for microhabitats with higher net rate of energy intake (NREI) were modulated by reach-scale macrophyte coverage, higher coverage increasing preferences for higher NREI. Macrophyte coverage was a weak positive predictor for depth and NREI, and a weak negative predictor for water velocity and median substrate. Our results suggest trade-offs between fish predation risk and bioenergetic food intake, with macrophytes modulating these trade-offs across scales by affecting reach-scale geomorphology, bioenergetics, and predation risk. As such, this study highlights the important and dynamic role that macrophytes can play in fish population dynamics in rivers, with important implications for management decisions.


Citations (67)


... We found only small amounts of beaver-chewed sagebrush (Artemesia tridentata) inserted into our structures, possibly because upland woody species like sage are inaccessible and expose beavers to predation. The difficulties of structure maintenance faced by beavers in locations lacking woody riparian vegetation constitute another planning consideration, although artificial structures are only inconsistently adopted by beavers even when vegetation is more available (Nash et al. 2021;Sandbach et al. 2024), and human maintenance is considered part of BDA-based restoration (Castro et al. 2017). The hours that we invested in repair may represent a low estimate if extrapolated to other projects, both because we contracted an experienced restoration crew with prior work in a nearby system, Bridge ...

Reference:

Multiyear trajectories of stream and riparian responses to beaver dam analogs on a low-gradient channel lacking woody riparian vegetation
Beaver dam analogs did not improve beaver translocation outcomes in a desert river
  • Citing Article
  • February 2024

Restoration Ecology

... Although disruptions in the longitudinal sediment continuity are generally viewed poorly because they can affect the river system resilience to human disturbances (Wohl, 2017), the complete removal of grade control points in some circumstances can also lead to negative outcomes. Instructive examples include the benefits of valley "plug" formation in arid environments, which was observed by Remiszewski et al. (2023) to lead to a rapid increase in habitat diversity. Many studies have similarly demonstrated the role that wood jams can play in the formation of alluvial sections that are beneficial for fish habitat and for locally moderating the energy of flood flows (e.g., Montgomery et al., 1996;Wohl et al., 2019). ...

Expansive, positive changes to fish habitat diversity following the formation of a valley plug in a degraded desert river

River Research and Applications

... Low water velocity may cause ecosystem productivity to decrease due to a lesser energy contribution, thus affecting reproduction and survival. In addition, low velocity affects fish population dynamics and restricts habitat availability, impacting their populations and overall ecosystem health [55][56][57]. Regarding water quality, low velocity may lead to increasing nutrient concentration, turbidity, and chlorophyll levels, as well as expanded distribution and mixing processes [58][59][60]. Significant depth changes, reaching up to 1.5 m ( Figure 7B), were observed between seasons. ...

The scale-dependent role of submerged macrophytes as drift-feeding lotic fish habitat

... Dissolved oxygen (DO) is essential for sustaining aquatic life, including maintaining the well-being of fish and benthic communities [1][2][3][4]. Seasonal fluctuations in DO levels, where the minimum DO concentrations drop below 2 mg/L for extended periods, can significantly disrupt aquatic ecosystems. Recent studies emphasize the need to better understand and more accurately forecast DO concentrations, which are crucial for maintaining ecological balance and mitigating long-term environmental changes. ...

Drawdown, Habitat, and Kokanee Populations in a Western U.S. Reservoir
  • Citing Article
  • March 2023

North American Journal of Fisheries Management

... The Hovsgol grayling is ecologically similar to the Baikal grayling and Arctic grayling (Thymallus arcticus), which have both been predicted to decrease in their distributions, abundance, and growth in response to warming, based on a study in the Eg-Uur River, Mongolia (Hartman and Jensen 2017). Therefore, we conclude that declining size, which is among the most rapid declines in salmonid body size globally (Solokas et al. 2023), and CPUE of Hovsgol grayling during the period of our study could have been partially caused by climate change. ...

Shrinking body size and climate warming: Many freshwater salmonids do not follow the rule

Global Change Biology

... Furthermore, based on limited research, there is little correlation between dam density and beaver population abundance (Bradt 1938;Hay 1955;Swafford et al. 2003); beaver populations are not often measured, with dam density used as a proxy for beaver abundance in many studies. Therefore, the beaver population in the Price River may have been at or near carrying capacity prior to translocations (Doden et al. 2022b), although this seems unlikely when we compare the Price to nearby, ecologically similar rivers with high levels of obvious beaver activity (Remiszewski et al. 2022). Beavers are territorial and will often display conspecific aggression, especially in areas of high population density (Crawford et al. 2015;Mayer et al. 2020). ...

Expansive, positive changes to habitat diversity following the formation of a valley plug in a degraded desert river

... Since domestic animals and humans frequently visit the natural freshwater habitats of beavers, we believe that studying the diseases of this rodent might be useful for determining the health of freshwater ecosystems, as demonstrated for other aquatic animals [82,83]. Because beavers are ecosystem engineers, they have been historically translocated to facilitate the restoration of degraded ecosystems [84]. Our study and others [15,85] alert us to the potential risk of moving pathogens that might affect other beaver populations, native wildlife, domestic animals, and humans. ...

Comparing translocated beavers used as passive restoration tools to resident beavers in degraded desert rivers

... The same density-dependent demographic processes that support the sustainable harvest of fish and wildlife (Hilborn & Walters, 1992;Skalski et al., 2005) become a challenge for control programs as well-established, highly productive populations can recover or even increase following harvest-based control (Klein et al., 2022;Zipkin et al., 2009). Density-dependent processes including compensatory recruitment, survival, or immigration have often hindered the progress of invasive species control efforts and have been documented in the attempted suppression of plants (Hastings et al., 2006), mammals (Harding et al., 2001;Lieury et al., 2015;Melero et al., 2015), amphibians (Govindarajulu et al., 2005) and fish (Healy et al., 2022;Weber et al., 2016). To avoid allocating resources to ineffective management strategies, it is critical to evaluate how much effort long-term suppression of a population requires (Wallace & Walsworth, 2024). ...

Exploring metapopulation‐scale suppression alternatives for a global invader in a river network experiencing climate change

... Parasites such as Cryptosporidium spp., Giardia spp. [3,14,15], Toxoplasma gondii, and Sarcocystis neurona [15] are among the main water-borne protozoans infecting beavers in North America, while neural larva migrans (NLM) of Baylisascaris spp. has caused encephalitis in beavers and other rodents sharing the same niche with raccoons [16]. ...

Health Screening of American Beavers (Castor canadensis) in Utah, USA

Journal of Wildlife Diseases

... However, modifying dam operations to reduce entrainment or restore Lewis and Clark Lake's thermal regime is unlikely because Fort Randall Dam is a bottom-release dam with cold hypolimnetic discharges, and because competing interests related to hydroelectric power generation limit dam operations. Restoration of natural flow regimes are often constrained by societal demands for water that take precedence over fisheries objectives (Pennock et al. 2022). ...

Failure to achieve recommended environmental flows coincides with declining fish populations: Long‐term trends in regulated and unregulated rivers

Freshwater Biology