Publications by authors named "Phaedra Budy"

13 Publications

  • Page 1 of 1

Trophic niches of native and nonnative fishes along a river-reservoir continuum.

Sci Rep 2021 Jun 9;11(1):12140. Epub 2021 Jun 9.

Division of Biology, Kansas State University, Manhattan, KS, 66502, USA.

Instream barriers can constrain dispersal of nonnative fishes, creating opportunities to test their impact on native communities above and below these barriers. Deposition of sediments in a river inflow to Lake Powell, USA resulted in creation of a large waterfall prohibiting upstream movement of fishes from the reservoir allowing us to evaluate the trophic niche of fishes above and below this barrier. We expected niche overlap among native and nonnative species would increase in local assemblages downstream of the barrier where nonnative fish diversity and abundance were higher. Fishes upstream of the barrier had more distinct isotopic niches and species exhibited a wider range in δN relative to downstream. In the reservoir, species were more constrained in δN and differed more in δC, representing a shorter, wider food web. Differences in energetic pathways and resource availability among habitats likely contributed to differences in isotopic niches. Endangered Razorback Sucker (Xyrauchen texanus) aggregate at some reservoir inflows in the Colorado River basin, and this is where we found the highest niche overlap among species. Whether isotopic niche overlap among adult native and nonnative species has negative consequences is unclear, because data on resource availability and use are lacking; however, these observations do indicate the potential for competition. Still, the impacts of diet overlap among trophic generalists, such as Razorback Sucker, are likely low, particularly in habitats with diverse and abundant food bases such as river-reservoir inflows.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-021-91730-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8190098PMC
June 2021

Investigating the morphological and genetic divergence of arctic char ( populations in lakes of arctic Alaska.

Ecol Evol 2021 Apr 5;11(7):3040-3057. Epub 2021 Mar 5.

Department of Watershed Sciences and the Ecology Center Utah State University Logan UT USA.

Polymorphism facilitates coexistence of divergent morphs (e.g., phenotypes) of the same species by minimizing intraspecific competition, especially when resources are limiting. Arctic char ( sp.) are a Holarctic fish often forming morphologically, and sometimes genetically, divergent morphs. In this study, we assessed the morphological and genetic diversity and divergence of 263 individuals from seven populations of arctic char with varying length-frequency distributions across two distinct groups of lakes in northern Alaska. Despite close geographic proximity, each lake group occurs on landscapes with different glacial ages and surface water connectivity, and thus was likely colonized by fishes at different times. Across lakes, a continuum of physical (e.g., lake area, maximum depth) and biological characteristics (e.g., primary productivity, fish density) exists, likely contributing to characteristics of present-day char populations. Although some lakes exhibit bimodal size distributions, using model-based clustering of morphometric traits corrected for allometry, we did not detect morphological differences within and across char populations. Genomic analyses using 15,934 SNPs obtained from genotyping by sequencing demonstrated differences among lake groups related to historical biogeography, but within lake groups and within individual lakes, genetic differentiation was not related to total body length. We used PERMANOVA to identify environmental and biological factors related to observed char size structure. Significant predictors included water transparency (i.e., a primary productivity proxy), char density (fish·ha), and lake group. Larger char occurred in lakes with greater primary production and lower char densities, suggesting less intraspecific competition and resource limitation. Thus, char populations in more productive and connected lakes may prove more stable to environmental changes, relative to food-limited and closed lakes, if lake productivity increases concomitantly. Our findings provide some of the first descriptions of genomic characteristics of char populations in arctic Alaska, and offer important consideration for the persistence of these populations for subsistence and conservation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.7211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8019052PMC
April 2021

Trophic structure of apex fish communities in closed versus leaky lakes of arctic Alaska.

Oecologia 2020 Nov 15;194(3):491-504. Epub 2020 Oct 15.

Department of Watershed Sciences, The Ecology Center, Utah State University, 5210 Old Main Hill, Logan, UT, 84322-5210, USA.

Despite low species diversity and primary production, trophic structure (e.g., top predator species, predator size) is surprisingly variable among Arctic lakes. We investigated trophic structure in lakes of arctic Alaska containing arctic char Salvelinus alpinus using stomach contents and stable isotope ratios in two geographically-close but hydrologically-distinct lake clusters to investigate how these fish may interact and compete for limited food resources. Aside from different lake connectivity patterns ('leaky' versus 'closed'), differing fish communities (up to five versus only two species) between lake clusters allowed us to test trophic hypotheses including: (1) arctic char are more piscivorous, and thereby grow larger and obtain higher trophic positions, in the presence of other fish species; and, (2) between arctic char size classes, resource polymorphism is more prominent, and thereby trophic niches are narrower and overlap less, in the absence of other predators. Regardless of lake cluster, we observed little direct evidence of arctic char consuming other fishes, but char were larger (mean TL = 468 vs 264 mm) and trophic position was higher (mean TP = 4.0 vs 3.8 for large char) in lakes with other fishes. Further, char demonstrated less intraspecific overlap when other predators were present whereas niche overlap was up to 100% in closed, char only lakes. As hydrologic characteristics (e.g., lake connectivity, water temperatures) will change across the Arctic owing to climate change, our results provide insight regarding potential concomitant changes to fish interactions and increase our understanding of lake trophic structure to guide management and conservation goals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00442-020-04776-9DOI Listing
November 2020

BioTIME: A database of biodiversity time series for the Anthropocene.

Glob Ecol Biogeogr 2018 Jul 24;27(7):760-786. Epub 2018 Jul 24.

German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany.

Motivation: The BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.

Main Types Of Variables Included: The database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.

Spatial Location And Grain: BioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km (158 cm) to 100 km (1,000,000,000,000 cm).

Time Period And Grain: BioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.

Major Taxa And Level Of Measurement: BioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.

Software Format: .csv and .SQL.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/geb.12729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6099392PMC
July 2018

Flow management and fish density regulate salmonid recruitment and adult size in tailwaters across western North America.

Ecol Appl 2015 Dec;25(8):2168-79

Rainbow and brown trout have been intentionally introduced into tailwaters downriver of dams globally and provide billions of dollars in economic benefits. At the same time, recruitment and maximum length of trout populations in tailwaters often fluctuate erratically, which negatively affects the value of fisheries. Large recruitment events may increase dispersal downriver where other fish species may be a priority (e.g., endangered species). There is an urgent need to understand the drivers of trout population dynamics in tailwaters, in particular the role of flow management. Here, we evaluate how flow, fish density, and other physical factors of the river influence recruitment and mean adult length in tailwaters across western North America, using data from 29 dams spanning 1-19 years. Rainbow trout recruitment was negatively correlated with high annual, summer, and spring flow and dam latitude, and positively correlated with high winter flow, subadult brown trout catch, and reservoir storage capacity. Brown trout recruitment was negatively correlated with high water velocity and daily fluctuations in flow (i.e., hydropeaking) and positively correlated with adult rainbow trout catch. Among these many drivers, rainbow trout recruitment was primarily correlated with high winter flow combined with low spring flow, whereas brown trout recruitment was most related to high water velocity. The mean lengths of adult rainbow and brown trout were influenced by similar flow and catch metrics. Length in both species was positively correlated with high annual flow but declined in tailwaters with high daily fluctuations in flow, high catch rates of conspecifics, and when large cohorts recruited to adult size. Whereas brown trout did not respond to the proportion of water allocated between seasons, rainbow trout length increased in rivers that released more water during winter than in spring. Rainbow trout length was primarily related to high catch rates of conspecifics, whereas brown trout length was mainly related to large cohorts recruiting to the adult size class. Species-specific responses to flow management are likely attributable to differences in seasonal timing of key life history events such as spawning, egg hatching, and fry emergence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1890/14-2211.1DOI Listing
December 2015

An occupancy-based quantification of the highly imperiled status of desert fishes of the southwestern United States.

Conserv Biol 2015 Aug 21;29(4):1142-52. Epub 2015 Apr 21.

Department of Watershed Sciences, Utah State University, Logan, Utah, 84322-5210, U.S.A.

Desert fishes are some of the most imperiled vertebrates worldwide due to their low economic worth and because they compete with humans for water. An ecological complex of fishes, 2 suckers (Catostomus latipinnis, Catostomus discobolus) and a chub (Gila robusta) (collectively managed as the so-called three species) are endemic to the U.S. Colorado River Basin, are affected by multiple stressors, and have allegedly declined dramatically. We built a series of occupancy models to determine relationships between trends in occupancy, local extinction, and local colonization rates, identify potential limiting factors, and evaluate the suitability of managing the 3 species collectively. For a historical period (1889-2011), top performing models (AICc) included a positive time trend in local extinction probability and a negative trend in local colonization probability. As flood frequency decreased post-development local extinction probability increased. By the end of the time series, 47% (95% CI 34-61) and 15% (95% CI 6-33) of sites remained occupied by the suckers and the chub, respectively, and models with the 2 species of sucker as one group and the chub as the other performed best. For a contemporary period (2001-2011), top performing (based on AICc ) models included peak annual discharge. As peak discharge increased, local extinction probability decreased and local colonization probability increased. For the contemporary period, results of models that split all 3 species into separate groups were similar to results of models that combined the 2 suckers but not the chub. Collectively, these results confirmed that declines in these fishes were strongly associated with water development and that relative to their historic distribution all 3 species have declined dramatically. Further, the chub was distinct in that it declined the most dramatically and therefore may need to be managed separately. Our modeling approach may be useful in other situations in which targeted data are sparse and conservation status and best management approach for multiple species are uncertain.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/cobi.12513DOI Listing
August 2015

Application of science-based restoration planning to a desert river system.

Environ Manage 2015 Jun 8;55(6):1246-61. Epub 2015 Apr 8.

Department of Watershed Sciences, The Ecology Center, Utah State University, 5210 Old Main Hill, Logan, UT, 84322, USA,

Persistence of many desert river species is threatened by a suite of impacts linked to water infrastructure projects that provide human water security where water is scarce. Many desert rivers have undergone regime shifts from spatially and temporally dynamic ecosystems to more stable systems dominated by homogenous physical habitat. Restoration of desert river systems could aid in biodiversity conservation, but poses formidable challenges due to multiple threats and the infeasibility of recovery to pre-development conditions. The challenges faced in restoring desert rivers can be addressed by incorporating scientific recommendations into restoration planning efforts at multiple stages, as demonstrated here through an example restoration project. In particular, use of a watershed-scale planning process can identify data gaps and irreversible constraints, which aid in developing achievable restoration goals and objectives. Site-prioritization focuses limited the resources for restoration on areas with the greatest potential to improve populations of target organisms. Investment in research to understand causes of degradation, coupled with adoption of a guiding vision is critical for identifying feasible restoration actions that can enhance river processes. Setting monitoring as a project goal, developing hypotheses for expected outcomes, and implementing restoration as an experimental design will facilitate adaptive management and learning from project implementation. Involvement of scientists and managers during all planning stages is critical for developing process-based restoration actions and an implementation plan to maximize learning. The planning process developed here provides a roadmap for use of scientific recommendations in future efforts to recover dynamic processes in imperiled riverine ecosystems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00267-015-0481-5DOI Listing
June 2015

Assessing the likely effectiveness of multispecies management for imperiled desert fishes with niche overlap analysis.

Conserv Biol 2015 Aug 27;29(4):1153-63. Epub 2015 Jan 27.

Department of Watershed Sciences, The Ecology Center, Utah State University, 5210 Old Main Hill, Logan, UT, 84322, U.S.A.

A critical decision in species conservation is whether to target individual species or a complex of ecologically similar species. Management of multispecies complexes is likely to be most effective when species share similar distributions, threats, and response to threats. We used niche overlap analysis to assess ecological similarity of 3 sensitive desert fish species currently managed as an ecological complex. We measured the amount of shared distribution of multiple habitat and life history parameters between each pair of species. Habitat use and multiple life history parameters, including maximum body length, spawning temperature, and longevity, differed significantly among the 3 species. The differences in habitat use and life history parameters among the species suggest they are likely to respond differently to similar threats and that most management actions will not benefit all 3 species equally. Habitat restoration, frequency of stream dewatering, non-native species control, and management efforts in tributaries versus main stem rivers are all likely to impact each of the species differently. Our results demonstrate that niche overlap analysis provides a powerful tool for assessing the likely effectiveness of multispecies versus single-species conservation plans.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/cobi.12457DOI Listing
August 2015

Understanding how lake populations of arctic char are structured and function with special consideration of the potential effects of climate change: a multi-faceted approach.

Oecologia 2014 Sep 27;176(1):81-94. Epub 2014 Jun 27.

U.S. Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed Sciences, and The Ecology Center, Utah State University, Logan, UT, 84322, USA,

Size dimorphism in fish populations, both its causes and consequences, has been an area of considerable focus; however, uncertainty remains whether size dimorphism is dynamic or stabilizing and about the role of exogenous factors. Here, we explored patterns among empirical vital rates, population structure, abundance and trend, and predicted the effects of climate change on populations of arctic char (Salvelinus alpinus) in two lakes. Both populations cycle dramatically between dominance by small (≤300 mm) and large (>300 mm) char. Apparent survival (Φ) and specific growth rates (SGR) were relatively high (40-96%; SGR range 0.03-1.5%) and comparable to those of conspecifics at lower latitudes. Climate change scenarios mimicked observed patterns of warming and resulted in temperatures closer to optimal for char growth (15.15 °C) and a longer growing season. An increase in consumption rates (28-34%) under climate change scenarios led to much greater growth rates (23-34%). Higher growth rates predicted under climate change resulted in an even greater predicted amplitude of cycles in population structure as well as an increase in reproductive output (Ro) and decrease in generation time (Go). Collectively, these results indicate arctic char populations (not just individuals) are extremely sensitive to small changes in the number of ice-free days. We hypothesize years with a longer growing season, predicted to occur more often under climate change, produce elevated growth rates of small char and act in a manner similar to a "resource pulse," allowing a sub-set of small char to "break through," thus setting the cycle in population structure.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00442-014-2993-8DOI Listing
September 2014

Limitation and facilitation of one of the world's most invasive fish: an intercontinental comparison.

Ecology 2013 Feb;94(2):356-67

U.S. Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed Sciences, Utah State University, Logan, Utah 84322-5210, USA.

Purposeful species introductions offer opportunities to inform our understanding of both invasion success and conservation hurdles. We evaluated factors determining the energetic limitations of brown trout (Salmo trutta) in both their native and introduced ranges. Our focus was on brown trout because they are nearly globally distributed, considered one of the world's worst invaders, yet imperiled in much of their native habitat. We synthesized and compared data describing temperature regime, diet, growth, and maximum body size across multiple spatial and temporal scales, from country (both exotic and native habitats) and major geographic area (MGA) to rivers and years within MGA. Using these data as inputs, we next used bioenergetic efficiency (BioEff), a relative scalar representing a realized percentage of maximum possible consumption (0-100%) as our primary response variable and a multi-scale, nested, mixed statistical model (GLIMMIX) to evaluate variation among and within spatial scales and as a function of density and elevation. MGA and year (the residual) explained the greatest proportion of variance in BioEff. Temperature varied widely among MGA and was a strong driver of variation in BioEff. We observed surprisingly little variation in the diet of brown trout, except the overwhelming influence of the switch to piscivory observed only in exotic MGA. We observed only a weak signal of density-dependent effects on BioEff; however, BioEff remained < 50% at densities > 2.5 fish/m2. The trajectory of BioEff across the life span of the fish elucidated the substantial variation in performance among MGAs; the maximum body size attained by brown trout was consistently below 400 mm in native habitat but reached approximately 600 mm outside their native range, where brown trout grew rapidly, feeding in part on naive prey fishes. The integrative, physiological approach, in combination with the intercontinental and comparative nature of our study, allowed us to overcome challenges associated with context-dependent variation in determining invasion success. Overall our results indicate "growth plasticity across the life span" was important for facilitating invasion, and should be added to lists of factors characterizing successful invaders.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1890/12-0628.1DOI Listing
February 2013

Unintended consequences of restoration: loss of riffles and gravel substrates following weir installation.

J Environ Manage 2012 Oct 21;109:154-63. Epub 2012 Jun 21.

Intermountain Center for River Rehabilitation and Restoration, Department of Watershed Sciences, Utah State University, 5210 Old Main Hill, Logan, UT 84322-5210, USA.

We used pre- and post-restoration channel surveys of the Donner und Blitzen River, Oregon, to evaluate the effects of grade-control structures on channel morphology and baseflow habitat conditions for native redband trout and other aquatic biota. Six years after installation, we found that the channel had a smaller proportion of riffles and pools and less gravel substrate, combined with an increase in the proportion of flat waters and consolidated clay on the bed surface. Both local scour downstream from weirs and backwater effects upstream from weirs appear to have caused the general flattening and fining of the channel. A direct-step backwater calculation indicates that backwaters extended to the upstream weir at both low and high flows, creating long sections of flat water separated by short, steep drops. Despite backwater effects, a comparison of longitudinal profiles before and six years after weir installation showed bed erosion downstream of nearly all weirs, likely a consequence of the cohesive clay material that dominates the channel bed and banks. A deep inner channel reflects the cohesive nature of the clay and the mechanisms of abrasion, and indicates that sediment load is low relative to the transport capacity of the flow. Unfortunately, weirs were problematic in this system because of the cohesive clay substrate, limited sediment supply, and low channel gradient. Although deeper flows due to backwaters might be more favorable for resident trout, less gravel and fewer riffles are likely to negatively impact trout spawning habitat, macroinvertebrate communities, and biofilm productivity. Our results demonstrate the potential limitations of a single-feature approach to restoration that may be ineffective for a given geomorphic context and may overlook other aspects of the ecosystem. We highlight the need to incorporate geomorphic characteristics of a system into project design and predictions of system response.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jenvman.2012.05.013DOI Listing
October 2012

Predicting fish growth potential and identifying water quality constraints: a spatially-explicit bioenergetics approach.

Environ Manage 2011 Oct 17;48(4):691-709. Epub 2011 Jul 17.

US Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed Sciences, Utah State University, 5210 Old Main Hill, Logan, UT, 84322-5210, USA.

Anthropogenic impairment of water bodies represents a global environmental concern, yet few attempts have successfully linked fish performance to thermal habitat suitability and fewer have distinguished co-varying water quality constraints. We interfaced fish bioenergetics, field measurements, and Thermal Remote Imaging to generate a spatially-explicit, high-resolution surface of fish growth potential, and next employed a structured hypothesis to detect relationships among measures of fish performance and co-varying water quality constraints. Our thermal surface of fish performance captured the amount and spatial-temporal arrangement of thermally-suitable habitat for three focal species in an extremely heterogeneous reservoir, but interpretation of this pattern was initially confounded by seasonal covariation of water residence time and water quality. Subsequent path analysis revealed that in terms of seasonal patterns in growth potential, catfish and walleye responded to temperature, positively and negatively, respectively; crappie and walleye responded to eutrophy (negatively). At the high eutrophy levels observed in this system, some desired fishes appear to suffer from excessive cultural eutrophication within the context of elevated temperatures whereas others appear to be largely unaffected or even enhanced. Our overall findings do not lead to the conclusion that this system is degraded by pollution; however, they do highlight the need to use a sensitive focal species in the process of determining allowable nutrient loading and as integrators of habitat suitability across multiple spatial and temporal scales. We provide an integrated approach useful for quantifying fish growth potential and identifying water quality constraints on fish performance at spatial scales appropriate for whole-system management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00267-011-9717-1DOI Listing
October 2011

Evaluating tributary restoration potential for Pacific salmon recovery.

Ecol Appl 2007 Jun;17(4):1068-86

U.S. Geological Survey, Utah Cooperative Fish and Wildlife Research Unit, Department of Watershed Sciences, 5210 Old Main Hill, Utah State University, Logan, Utah 84322-5210, USA.

Although habitat restoration can play a key role in the conservation of imperiled species, for animals that demonstrate long migrations and complex life histories, reliance on physical restoration of isolated habitat patches comes with considerable uncertainty. Nevertheless, within freshwater ecosystems, stream restoration has become a major conservation focus, with millions of dollars spent annually on efforts aimed at recovering degraded habitat and imperiled riverine species. Within this context, we addressed fundamental uncertainties of the focus on tributary restoration for recovery of salmon: (1) Is there potential for improving habitat in tributaries? (2) What magnitude of early survival improvement can be expected based on stream restoration? and (3) Will incremental increases in early survival be sufficient to ensure viability overall? We combined simple mechanistic habitat models, population viability measures, and categorical filters to quantify "restoration potential," expressed as increased total life-cycle survival in response to restored tributary condition, across 32 populations composing five major population groups (MPG). A wide gap remains between how much survival improvement is needed vs. what is likely to occur; restoration potential meets the necessary minimum increase needed for only four populations within one MPG. The remaining populations (84%, 4 MPG) still fall far below the survival increase needed for future viability. In addition, across all populations and groups, a 171% increase (on average) in total life-cycle survival is needed; only approximately 106% appears possible. A recovery strategy for these salmon that relies largely on tributary restoration to mitigate for known mortality imposed at other life stages (e.g., migration through hydropower dams) is risky with a low probability of success. We demonstrate an approach for completing an a priori evaluation of restoration potential linked to population viability, such that habitat restoration efforts can be biologically prioritized and scarce resources can be allocated to efforts with the greatest potential and the least amount of risk, in terms of meeting conservation and recovery goals.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1890/06-0022DOI Listing
June 2007