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USGS2014

Raft and floating radio frequency identification (RFID) antenna systems for detecting and estimating abundance of PIT-tagged fish in rivers

Portable radio frequency identification (RFID) PIT tag antenna systems are increasingly being used in studies examining aquatic animal movement, survival, and habitat use, and their design flexibility permits application in a wide variety of settings. We describe the construction, use, and performance of two portable floating RFID PIT tag antenna systems designed to detect fish that were unavailable for recapture using stationary antennas or electrofishing. A raft antenna system was designed to detect and locate PIT-tagged fish in relatively long (i.e., ≥10 km) river reaches, and consisted of two antennas: (1) a horizontal antenna (4 × 1.2 m) installed on the bottom of the raft and used to detect fish in shallower river reaches (<1 m), and (2) a vertical antenna (2.7 × 1.2 m) for detecting fish in deeper pools (≥1 m). Detection distances of the horizontal antenna were between 0.7 and 1.0 m, and detection probability was 0.32 ± 0.02 (mean ± SE) in a field test using rocks marked with 32-mm PIT tags. Detection probability of PIT-tagged fish in the Cache la Poudre River, Colorado, using the raft antenna system, which covered 21% of the wetted area, was 0.14 ± 0.14. A shore-deployed floating antenna (14.6 × 0.6 m), which covered 100% of the wetted area, was designed for use by two operators for detecting and locating PIT-tagged fish in shorter (i.e., <2 km) river reaches. Detection distances of the shore-deployed floating antenna were between 0.7 and 0.8 m, and detection probabilities during field deployment in the St. Vrain River exceeded 0.52. The shore-deployed floating antenna was also used to estimate abundance of PIT-tagged fish. Results suggest that the shore-deployed floating antenna could be used as an alternative to estimating abundance using traditional sampling methods such as electrofishing.

Colorado↗

USGS2014

Importance of understanding landscape biases in USGS gage locations: Implications and solutions for managers

Flow and water temperature are fundamental properties of stream ecosystems upon which many freshwater resource management decisions are based. U.S. Geological Survey (USGS) gages are the most important source of streamflow and water temperature data available nationwide, but the degree to which gages represent landscape attributes of the larger population of streams has not been thoroughly evaluated. We identified substantial biases for seven landscape attributes in one or more regions across the conterminous United States. Streams with small watersheds (<10 km 2 ) and at high elevations were often underrepresented, and biases were greater for water temperature gages and in arid regions. Biases can fundamentally alter management decisions and at a minimum this potential for error must be acknowledged accurately and transparently. We highlight three strategies that seek to reduce bias or limit errors arising from bias and illustrate how one strategy, supplementing USGS data, can greatly reduce bias.

Fisheries↗

USGS2016

Applications of genetic data to improve management and conservation of river fishes and their habitats

Environmental variation and landscape features affect ecological processes in fluvial systems; however, assessing effects at management-relevant temporal and spatial scales is challenging. Genetic data can be used with landscape models and traditional ecological assessment data to identify biodiversity hotspots, predict ecosystem responses to anthropogenic effects, and detect impairments to underlying processes. We show that by combining taxonomic, demographic, and genetic data of species in complex riverscapes, managers can better understand the spatial and temporal scales over which environmental processes and disturbance influence biodiversity. We describe how population genetic models using empirical or simulated genetic data quantify effects of environmental processes affecting species diversity and distribution. Our summary shows that aquatic assessment initiatives that use standardized data sets to direct management actions can benefit from integration of genetic data to improve the predictability of disturbance–response relationships of river fishes and their habitats over a broad range of spatial and temporal scales.

Fisheries↗

USGS2016

StreamThermal: A software package for calculating thermal metrics from stream temperature data

Improving quality and better availability of continuous stream temperature data allows natural resource managers, particularly in fisheries, to understand associations between different characteristics of stream thermal regimes and stream fishes. However, there is no convenient tool to efficiently characterize multiple metrics reflecting stream thermal regimes with the increasing amount of data. This article describes a software program packaged as a library in R to facilitate this process. With this freely-available package, users will be able to quickly summarize metrics that describe five categories of stream thermal regimes: magnitude, variability, frequency, timing, and rate of change. The installation and usage instruction of this package, the definition of calculated thermal metrics, as well as the output format from the package are described, along with an application showing the utility for multiple metrics. We believe this package can be widely utilized by interested stakeholders and greatly assist more studies in fisheries.

Fisheries↗

USGS2017

Synopsis of the Fourth International Percid Fishes Symposia

Percids play an integral role in food webs and freshwater fisheries of the world. Anthropogenic stressors such as pollution, overfishing, invasive species, and climate change threaten percid diversity and the sustainability of economically important fisher-ies. The International Percid Fish Symposium is the only scien-tific conference dedicated to this family of fishes, offering unique opportunities for communication, discussion, and collaboration among scientists studying these valuable fishes. In this synopsis, we review the history of the percid symposia with an emphasis on the recent Fourth International Percid Fish Symposium held in Tartu, Estonia, during April 2016 and discuss future needs and direction for this important scientific conference.

Fisheries↗

USGS2012

Disparate stakeholder management: the case of elk and bison feeding in southern Greater Yellowstone

For resource decisions to make the most possible progress toward achieving agency mandates, managers must work with stakeholders and may need to at least partially accommodate some of their key underlying interests. To accommodate stakeholder interests, while also substantively working toward fulfilling legal mandates, managers must understand the sociopolitical factors that influence the decision-making process. We coin the phrase disparate stakeholder management (DSM) to describe situations with disparate stakeholders and disparate management solutions. A DSM approach (DSMA) requires decision makers to combine concepts from many sciences, thus releasing them from disciplinary bonds that often constrain innovation and effectiveness. We combined three distinct approaches to develop a DSMA that assisted in developing a comprehensive range of elk and bison management alternatives in the Southern Greater Yellowstone Area. The DSMA illustrated the extent of compromise between meeting legal agency mandates and accommodating the preferences of certain stakeholder groups.

Wyoming↗

USGS2013

Reduced Myxobolus cerebralis actinospore production in a Colorado reservior may be linked to changes in Tubifex tubifex population structure

Elucidating the dynamics of a parasitic infection requiring two hosts in a natural ecosystem can be a daunting task. Myxobolus cerebralis (Mc), the myxozoan parasite that causes whirling disease in some salmonids, was detected in the Colorado River upstream of Windy Gap Reservoir (WGR) in 1988. Subsequently, whirling disease was implicated in the decline of wild Rainbow Trout Oncorhynchus mykiss in the river when WGR was identified as a point source of Mc triactinomyxons (TAMs). Between 1997 and 2004, numerous investigations began to elucidate the etiology of Mc in WGR. During this period, Mc TAM production in WGR declined more than 90%. Explanations for the decline have included differences in stream discharge between years, changes in the thermal regime of the lake, severe drought, changes in the fish population structure in WGR, and reductions in the prevalence and severity of Mc infection in salmonids in the Colorado and Fraser rivers upstream of WGR. All of these have been discredited as explanations for the reduced TAM production. In 2005, a new study was conducted to replicate the studies completed in 1998. In this paper, the results of a new real-time polymerase chain reaction assay utilized to quantify the mitochondrial 16S rDNA specific to each of four lineages of Tubifex tubifex in pooled samples of 50 oligochaetes are presented. These results suggest that compared with 1998, the densities of aquatic oligochaetes and T. tubifex have increased, TAM production has been greatly reduced, and the decline is congruent with the dominance of lineages I, V, and VI of T. tubifex—three lineages that are refractory or highly resistant to Mc infection—in the oligochaete population. While it is possible that the resistant lineages function as biofilters that deactivate Mc myxospores, the reason for the decline in TAM production in WGR remains an enigma.

Colorado↗

USGS2025

Environmental controls of suppressed fall crop productivity in an agrivoltaic solar array

Globally, agrivoltaics (AV) research has revealed how microclimates created by photovoltaic (PV) panels can be leveraged to promote reciprocal benefits for agricultural land use and PV energy generation. Yet, in regions of the United States where emissions reduction laws are likely to lead to greater PV development on croplands, empirical evaluation of such co-location remain under explored. Furthermore, the most common approach to AV in the United States is one that maximizes energy generation and secondarily accommodates for agricultural management, and the controls of crop production in facilities that employ such an approach are underrepresented in the AV literature. Here, we assessed the agronomic and physiological response of two vegetable crops (radish and radicchio) with different carbon allocation patterns (belowground and aboveground, respectively) in an energy focused AV facility during a fall growing season, in New York, United States. We found that a reduction in total irradiance (−24%) within the AV array decreased total biomass in both crop types (46% and 49%), with significant alterations to root-shoot ratios in radish. Reductions in total biomass were not a result of physiological acclimation, indicating that AV crops had similar photosynthetic capacity as control crops; however, the environmental constraints imposed by energy focused AV design (i.e. reduced irradiance) limited C uptake overall. Our findings highlight the need for novel management approaches (e.g. earlier planting of AV fall crops) to help overcome yield penalties incurred by energy focused AV designs.

New York↗

USGS2025

Pesticide concentrations in multiple physical and biological stream matrices are impacted by a bioenergy production facility receiving pesticide coated corn seeds

Insecticide and fungicide seed coatings have become prevalent in conventional agriculture in recent decades. From 2015 to 2021, the AltEn bioenergy plant (Mead, Nebraska, USA) generated ethanol from almost 100% unused/expired treated corn seeds. This use of these seeds for ethanol production resulted in the accumulation of large amounts of contaminated wastewater and solid residue, a portion of which was applied to surrounding farmland. To better understand the potential long-term environmental effects from the processing of treated seeds at this facility, five nearby stream sites were sampled in 2022 after the closure of the plant; these included two sites directly impacted by AltEn, one upstream, and two downstream of the impacted sites. Water and sediment were collected in March through July, and algae and fish samples were collected in July for chemical analysis. Overall, 60 pesticide compounds (parents and transformation products) were detected in one or more matrices, including 23 fungicides, 20 insecticides, 16 herbicides, and 1 bacterial growth inhibitor. Pesticide results (maximum detection frequency, maximum concentration) varied substantially by environmental compartment: water (100% multiple pesticides; 4,600 ng L −1 thiamethoxam transformation product (NOA-407475)), algae (100% multiple pesticides, 190 ng g −1 atrazine), sediment (60% dithiopyr, 2.3 ng g −1 acetochlor) and fish (20% pyraclostrobin, 2.2 ng g −1 atrazine). Pesticides associated with treated corn seeds (e.g., insecticides clothianidin, thiamethoxam; fungicides fluoxastrobin, thiabendazole) were detected at significantly higher concentrations ( p < 0.05) in stream water from sites impacted by the AltEn facility compared to non-impacted sites. Study results indicate that pesticides associated with the AltEn facility continue to be a source of contaminants to aquatic systems after the plant’s closure in 2021.

Environmental Toxicology and Chemistry↗

USGS2026

Beyond technical expertise: The role of mindset, interpersonal, and intrapersonal skills in the development of fisheries professionals

Objective Recognized as essential components for success, mindset and inter- and intrapersonal skills (often referred to as soft skills) play a crucial role in the growth and effectiveness of individuals throughout their careers. Individuals with strong inter- and intrapersonal skills and a mindset open to growth can efficiently navigate complex challenges that may involve working with diverse stakeholder groups, managing interdisciplinary teams, or resolving conflicts in ways that allow them to excel beyond their technical skill sets. Although formal education of natural resources professionals (and many other professions) generally prioritizes technical skills, cultivating inter- and intrapersonal skills and a growth mindset is critical to success. Methods Drawing on presentations and discussion from an early-career symposium at the 2023 American Fisheries Society Conference, we summarize skill sets valuable for success in fisheries and natural resources. Results We provide an overview of the roles mindset and inter- and intrapersonal skills have in developing a career, how to use these competencies to navigate natural resources professions, and actions for enhancing personal skills. This paper aims to provide a compendium of information and lessons learned from natural resources professionals with diverse experiences and to emphasize familiar concepts to help formalize their discussion in the fisheries profession. Conclusion Fisheries and other natural resource fields have become increasingly interdisciplinary, necessitating a broad suite of skills to effectively communicate across disciplines, convey multiple data types, and make decisions to address complex problems. Inter- and intrapersonal skill sets are foundational to successfully navigating the fisheries profession. Moreover, personal skills transcend our profession into our everyday lives, thus strengthening personal skills is a worthy endeavor.

Fisheries↗

USGS2016

3-D P- and S-wave velocity structure and low-frequency earthquake locations in the Parkfield, California region

To refine the 3-D seismic velocity model in the greater Parkfield, California region, a new data set including regular earthquakes, shots, quarry blasts and low-frequency earthquakes (LFEs) was assembled. Hundreds of traces of each LFE family at two temporary arrays were stacked with time–frequency domain phase weighted stacking method to improve signal-to-noise ratio. We extend our model resolution to lower crustal depth with LFE data. Our result images not only previously identified features but also low velocity zones (LVZs) in the area around the LFEs and the lower crust beneath the southern Rinconada Fault. The former LVZ is consistent with high fluid pressure that can account for several aspects of LFE behaviour. The latter LVZ is consistent with a high conductivity zone in magnetotelluric studies. A new Vs model was developed with S picks that were obtained with a new autopicker. At shallow depth, the low Vs areas underlie the strongest shaking areas in the 2004 Parkfield earthquake. We relocate LFE families and analyse the location uncertainties with the NonLinLoc and tomoDD codes. The two methods yield similar results.

California↗

USGS2021

Outside the box: Working with wildlife in biocontainment

Research with captive wildlife in Animal Biosafety Level 2 (ABSL2) and 3 (ABSL3) facilities is becoming increasingly necessary as emerging and re-emerging diseases involving wildlife have increasing impacts on human, animal, and environmental health. Utilizing wildlife species in a research facility often requires outside the box thinking with specialized knowledge, practices, facilities, and equipment. The USGS National Wildlife Health Center (NWHC) houses an ABSL3 facility dedicated to understanding wildlife diseases and developing tools to mitigate their impacts on animal and human health. This review presents considerations for utilizing captive wildlife for infectious disease studies, including, husbandry, animal welfare, veterinary care, and biosafety. Examples are drawn from primary literature review and collective 40-year experience of the NWHC. Working with wildlife in ABSL2 and ABSL3 facilities differs from laboratory animals in that typical laboratory housing systems, husbandry practices, and biosafety practices are not designed for work with wildlife. This requires thoughtful adaptation of standard equipment and practices, invention of customized solutions and development of appropriate enrichment plans using the natural history of the species and the microbiological characteristics of introduced and native pathogens. Ultimately, this task requires critical risk assessment, understanding of the physical and psychological needs of diverse species, creativity, innovation, and flexibility. Finally, continual reassessment and improvement are imperative in this constantly changing specialty area of infectious disease and environmental hazard research.

ILAR Journal↗

USGS2025

Non-lethal detection of Renibacterium salmoninarum in Greenback Cutthroat Trout Oncorhynchus clarkii stomias comparing mucus, blood, and ovarian fluid samples to kidney tissues

Objective Renibacterium salmoninarum , the causative agent of bacterial kidney disease, poses a major threat to both wild and aquaculture salmonid populations. Traditional detection methods typically involve lethal sampling to collect kidney tissues but are often impractical for species of conservation concern. This study evaluates nonlethal sampling techniques for detecting R. salmoninarum in Greenback Cutthroat Trout Oncorhynchus clarkii stomias by comparing mucus, blood, and ovarian fluid samples to conventional kidney tissue. Methods During the 2019 spawning season, we collected samples from 781 adult fish and tested for R. salmoninarum via direct fluorescent antibody test (DFAT) and quantitative polymerase chain reaction (qPCR). Results A total of 25 and 256 kidney tissues were positive by DFAT and qPCR, respectively. Of the three nonlethal samples tested, mucus swabs showed the highest percent correlation for detection with positive kidney tissues (DFAT = 47.6%, qPCR = 41.7%). Blood and ovarian fluid samples showed a lower percent correlation with positive kidney tissues (blood: DFAT = 12.0%, qPCR = 1.2%; ovarian fluid: DFAT = 12.5%, qPCR = 21.4%). Conclusions Our results suggest that nonlethal mucus swabbing could serve as a practical alternative for monitoring R. salmoninarum, especially in conservation efforts where minimizing fish mortality is critical.

Colorado↗

USGS2015

Population connectivity of endangered Ozark big-eared bats ( Corynorhinus townsendii ingens )

The endangered Ozark big-eared bat ( Corynorhinus townsendii ingens ) is restricted to eastern Oklahoma and western and north-central Arkansas, where populations may be susceptible to losses of genetic variation due to patchy distribution of colonies and potentially small effective population sizes. We used mitochondrial D-loop DNA sequences and 15 nuclear microsatellite loci to determine population connectivity among Ozark big-eared bat caves. Assessment of 7 caves revealed a haplotype not detected in a previous study (2002–2003) and gene flow among colonies in eastern Oklahoma. Our data suggest genetic mixing of individuals, which may be occurring at nearby swarming sites in the autumn. Further evidence of limited gene flow between caves in Oklahoma with a cave in Arkansas highlights the importance of including samples from geographically widespread caves to fully understand gene flow in this subspecies. It appears autumn swarming sites and winter hibernacula play an important role in providing opportunities for mating; therefore, we suggest protection of these sites, maternity caves, and surrounding habitat to facilitate gene flow among populations of Ozark big-eared bats.

Arkansas, Oklahoma↗

USGS2025

Hatchery rearing density affects poststocking survival

Objective Research has indicated that salmonids raised in a hatchery and stocked into the wild have lower future survival and reproductive success than wild fish. Understanding whether hatchery rearing practices affect populations after stocking can help to maximize the quality, quantity, and economic value of fish stocked for conservation and recreational purposes. The goal of our study was to test whether and to what extent rearing density affects poststocking survival of Rainbow Trout Oncorhynchus mykiss when stocked into a put-grow-and-take fishery. Methods Rainbow Trout were raised for 3 months in the hatchery at two densities (high = 51,948–13,072 fish/m 3 , rearing index 2.0, 1,260 metric units; low = 12,987–3,268 fish/m 3 , rearing index 0.5, 315 metric units). A subset of the fish were PIT-tagged and stocked into Parvin Lake, Red Feather Lakes, Colorado. Recaptures of tagged fish occurred every 2 weeks for the first 2 months poststocking and at 7 and 12 months poststocking. Results At the time of stocking, there were no statistical differences in Fulton’s condition factor, total length, weight, or hepatosomatic index for each treatment. Recapture data indicated that there was no difference in Fulton’s condition factor and hepatosomatic index after stocking. Apparent poststocking survival was higher for fish raised at low density in the hatchery compared with those raised at high density. Conclusions Our study suggests that rearing density affects fingerling Rainbow Trout poststocking survival. Stocking more fish due to fish being reared at higher densities within the hatchery did not result in more total fish remaining after a year in the lake compared with the low-density treatment. Rearing fish at high densities does not provide a benefit of more fish after stocking and may result in more disease risk in the hatchery.

Colorado↗

USGS2020

Parasites in marine food webs

Parasites have important and unique impacts on marine food webs. By infecting taxa across all trophic levels, parasites affect both bottom-up and top-down processes in marine systems. When host densities are high enough, parasites can regulate or even decimate their populations, causing regime shifts in marine systems. As consumers and resources, parasites are enmeshed in food webs in ways that are different from free-living species. Their unique lifestyle renders parasites more susceptible to perturbations than their free-living hosts. As a result, parasites serve as useful indicators of ecosystem integrity. A theory for how food webs affect parasites will help us better understand why a particular infectious disease has become problematic, give insight into how restoration might reduce a costly marine disease, or let us use parasites as indicators to follow changes in food-web complexity.

Book chapter↗

USGS2025

Riverscape genetics of nonnative Brook Trout to inform native cutthroat trout conservation

Objective Understanding how riverscape features influence gene flow is critical for managing population connectivity in freshwater species. We examined how landscape and stream characteristics shape the spatial genetic structure of nonnative Brook Trout Salvelinus fontinalis in a headwater stream network proposed for reintroduction of federally threatened Greenback Cutthroat Trout Oncorhynchus virginalis stomias . Brook Trout were studied to evaluate the suitability of this habitat for supporting a native trout metapopulation. Methods We genotyped 757 Brook Trout from 22 sites across a 60-km stream network using 12 microsatellite loci. Spatial genetic structure was assessed using clustering analysis (program STRUCTURE) and pairwise differentiation metrics ( F ST and Jost’s D ). A spatial network modeling approach was used to quantify the effects of riverscape features (e.g., stream gradient, stream order, waterfalls, and flow direction) on trout gene flow. Results Genetic clustering identified four distinct tributary groups, while estimates of pairwise genetic differentiation indicated some genetic connectivity across the network (mean F ST = 0.04; mean Jost’s D = 0.06). Trout gene flow was impeded by waterfalls, steep stream gradients, and increased hydrologic distance. Higher stream order and downstream flow direction were associated with stronger gene flow, and stream segments containing waterfalls and steeper gradients showed greater asymmetries between upstream and downstream gene flow. Conclusions Brook Trout populations in this stream network are spatially structured, but gene flow persists and is mediated by physical riverscape features and hydrologic distance. The observed patterns of genetic connectivity suggest that this habitat can support connectivity among populations of reintroduced Greenback Cutthroat Trout. In future native trout reintroduction efforts, prioritizing habitats with gradual stream gradients and fewer waterfalls would promote population connectivity.

Transactions of the American Fisheries Society↗

USGS2023

Conserved grasslands support similar pollinator diversity as pollinator-specific practice regardless of proximal cropland and pesticide exposure

Pollinator diversity and abundance are declining globally. Cropland agriculture and the corresponding use of agricultural pesticides may contribute to these declines, while increased pollinator habitat (flowering plants) can help mitigate them. Here we tested whether the relative effect of wildflower plantings on pollinator diversity and counts were modified by proportion of nearby agricultural land cover and pesticide exposure in 24 conserved grasslands in Iowa, USA. Compared with general grassland conservation practices, wildflower plantings led to only a 5% increase in pollinator diversity and no change in counts regardless of the proportion of cropland agriculture within a 1 km radius. Pollinator diversity increased earlier in the growing season and with per cent flower cover. Unexpectedly, neither insecticide nor total pesticide concentrations on above-ground passive samplers were related to pollinator diversity. However, pollinator community composition was most strongly related to date of sampling, total pesticide concentration, and forb or flower cover. Our results indicate very little difference in pollinator diversity between grassland conservation practices with and without wildflower plantings. Given the relatively high economic costs of wildflower plantings, our research provides initial evidence that investment in general grassland conservation may efficiently conserve pollinator diversity in temperate regions of intensive cropland agriculture.

Iowa↗