Geology topics

Research about United States

Source-linked reports with geographic coverage including United States.

At least 1,675 records · Page 93Linked to original sources

USGS2025

Shifting baselines of coral-reef species composition from the Late Pleistocene to the present in the Florida Keys

The ongoing global-scale reassembly of modern coral reefs is unprecedented compared with the observed stability of most late Quaternary reef assemblages. One notable exception is the marine isotope stage (MIS) 5e ( ca 130–116 thousand years ago [ka]) reefs in the Florida Keys, where the ubiquitous shallow-water coral, Acropora palmata , was near absent. Little is known, however, about reefs that grew during MIS5d–a ( ca 116–74 ka), between MIS5e and the Holocene. It is therefore unclear whether Florida's unique MIS5e coral assemblages represent a geologically brief anomaly or a more persistent departure from the western Atlantic coral-reef archetype. We addressed that question by reconstructing the composition of MIS5d–a reefs within 29 coral-reef cores collected throughout the Florida Keys. We then compared the relative composition of corals during MIS5d–a to existing datasets from MIS5e, Holocene and modern (1996 and 2022) reefs to evaluate how far today's reef assemblages have diverged from geological baselines. We show that although the proportion of reef frameworks built by corals was remarkably consistent ( ca 38%), species composition changed significantly through time. Acropora palmata was rare throughout MIS5, which we hypothesise was due to greater cold-temperature stress in Florida's subtropical reefs compared with the more climatically stable tropics. In contrast, the massive reef-building coral, Orbicella spp., was regionally dominant throughout the late Quaternary, but has become increasingly rare on modern reefs. By 2022, reefs in the Florida Keys were characterised by a truly novel coral assemblage dominated by Porites astreoides and Siderastrea siderea . In many ways, Florida's reefs defy the concept of a natural baseline; instead, their most persistent characteristic since the Late Pleistocene is their uniqueness. Yet, as reefs are increasingly subjected to unprecedented levels of environmental change, the exceptions to what was normal in the past could, paradoxically, provide the best geological analogues for the future.

Florida↗

USGS2025

Linking permafrost to the abundance, biomass, and energy density of fish in Arctic headwater streams

Permafrost thaw alters groundwater flow, river hydrology, stream-catchment interactions, and the availability of carbon and nutrients in headwater streams. The impact of permafrost on watershed hydrology and biogeochemistry of headwater streams has been demonstrated, but there is little understanding of how permafrost influences fish in these ecosystems. We examined relations among permafrost characteristics, the resulting changes in water temperature, stream hydrology (e.g., discharge flashiness), and macroinvertebrates, with the abundance, biomass, and energy density of juvenile Dolly Varden ( Salvelinus malma ) and Arctic Grayling ( Thymallus arcticus ) across 10 headwater streams in northwestern Alaska. Macroinvertebrate density was driven by concentrations of dissolved carbon and nutrients supporting stream food webs. Dolly Varden abundance was primarily related to water temperature with fewer fish in warmer streams, whereas Dolly Varden energy density decreased with the flashiness of the headwater streams. Dolly Varden biomass was related to both temperature and bottom-up food web effects. The energy density of Arctic Grayling decreased with warmer temperatures and discharge flashiness. These relations demonstrate the importance of terrestrial–aquatic connections in permafrost landscapes and indicate the complexity of landscape effects on fish. Because permafrost thaw is one of the most impactful changes occurring as the Arctic warms, an improved understanding of how stream temperature, hydrology, and bottom-up food web processes influence fish populations can aid forecasting of future conditions across the Arctic.

Alaska↗

USGS2025

Distribution and abundance of Least Bell’s Vireos (Vireo bellii pusillus) and Southwestern Willow Flycatchers (Empidonax traillii extimus) at the Mojave River Dam, San Bernardino County, California—2024 data summary

We surveyed for Least Bell’s Vireos ( Vireo bellii pusillus ; vireo) and Southwestern Willow Flycatchers ( Empidonax traillii extimus ; flycatcher) at the Mojave River Dam study area near Hesperia, California, in 2024. Four vireo surveys were completed between April 17 and July 2, 2024, and three flycatcher surveys were completed between May 23 and July 2, 2024. We detected three territorial male vireos, all of which were paired. No juveniles were observed during surveys. Vireo territories were reported in two habitat types: riparian scrub and willow-cottonwood. Red or arroyo willow ( Salix laevigata or lasiolepis ) was the dominant plant species in most vireo territories. No territorial or transient flycatchers were observed.

California↗

USGS2025

Fine-resolution satellite remote sensing improves spatially distributed snow modeling to near real time

Given the highly variable distribution of seasonal snowpacks in complex mountainous environments, the accurate snow modeling of basin-wide snow water equivalent (SWE) requires a spatially distributed approach at a sufficiently fine grid resolution (<500 m) to account for the important processes in the seasonal evolution of a snowpack (e.g., wind redistribution of snow to resolve patchy snow cover in an alpine zone). However, even well-validated snow evolution models, such as SnowModel, are prone to errors when key model inputs, such as the precipitation and wind speed and direction, are inaccurate or only available at coarse spatial resolutions. Incorporating fine-spatial-resolution remotely sensed snow-covered area (SCA) information into spatially distributed snow modeling has the potential to refine and improve fine-resolution snow water equivalent (SWE) estimates. This study developed 30 m resolution SnowModel simulations across the Big Thompson River, Fraser River, Three Lakes, and Willow Creek Basins, a total area of 4212 km 2 in Colorado, for the water years 2000–2023, and evaluated the incorporation of a Moderate Resolution Imaging Spectroradiometer (MODIS) and Landsat SCA datasets into the model’s development and calibration. The SnowModel was calibrated spatially to the Landsat mean annual snow persistence (SP) and temporally to the MODIS mean basin SCA using a multi-objective calibration procedure executed using Latin hypercube sampling and a stepwise calibration process. The Landsat mean annual SP was also used to further optimize the SnowModel simulations through the development of a spatially variable precipitation correction field. The evaluations of the SnowModel simulations using the Airborne Snow Observatories’ (ASO’s) light detection and ranging (lidar)-derived SWE estimates show that the versions of the SnowModel calibrated to the remotely sensed SCA had an improved performance (mean error ranging from −28 mm to −6 mm) compared with the baseline simulations (mean error ranging from 69 mm to 86 mm), and comparable spatial patterns to those of the ASO, especially at the highest elevations. Furthermore, this study’s results highlight how a regularly updated 30 m resolution SCA could be used to further improve the calibrated SnowModel simulations to near real time (latency of 5 days or less).

Colorado↗

USGS2025

Evidence of mineral alteration in a salt marsh subterranean estuary: Implications for carbon and trace element cycling

Subterranean estuaries (STE) in salt marshes are biogeochemically active zones where interactions between terrestrial groundwater and seawater drive complex cycling of carbon and trace elements, influenced by mineral dissolution. These systems, characterized by fine-grained organic-rich peat overlying permeable coastal aquifers, play a crucial role as a blue carbon sink, yet their geochemical dynamics remain poorly understood. We investigated dissolved trace elements, carbon, silica, and radium isotopes in a salt marsh STE (Sage Lot Pond, Waquoit Bay, MA) over seasonal and annual cycles. Our results reveal that groundwater and estuarine water circulation through marsh peat and aquifer sediments leads to enrichments of dissolved organic and inorganic carbon (DOC and DIC), Si, Ba, and Mn, with variable source/sink behavior of Fe and net removal of U. Submarine groundwater discharge dominated Ba fluxes, whereas pore water drainage from marsh peat acted as the main sink for U and source of Si. Fe cycling was variable, with terrestrial Fe largely removed as groundwater passed through the STE, consistent with Fe-sulfide and amorphous phase formation. Radium isotope ratios identified two distinct subsurface flow pathways, influenced by metal-oxide cycling and organic matter breakdown. Si production was decoupled from DIC, suggesting Si originates from mineral alteration, whereas DIC results from both mineral weathering and microbial respiration. Silicate mineral alteration, coupled with marsh pore water drainage, accounts for up to 16% of annual DIC exports (66 g C m −2 y −1 ), highlighting the importance of STEs in coastal carbon and trace element cycling, especially as marshes face environmental change.

Massachusetts↗

USGS2025

The complete mitochondrial genomes of the freshwater mussel Ortmanniana ligamentina (Lamarck, 1819): male and female mitotypes

Freshwater mussels of the Unionida order are important to freshwater ecosystems but are highly imperiled worldwide. Improving our understanding of these species is crucial to their continued conservation. Some Unionid mussels exhibit double uniparental inheritance (DUI) in which individuals have two mitochondrial genomes. Of those species with DUI, sequences of the female mitotype are most prevalent in genetic databases. Here, we demonstrate the ability to recover both mitotypes of Ortmanniana ligamentina (Lamarck, 1819) from a non-lethal collection method coupled with high-throughput sequencing. Increased male mitotype sequence representation facilitates understanding Unionid genetic diversity and development of molecular tools for species detection.

Missouri, Pennsylvania↗

USGS2025

Evaluating episodic sediment deposition zones in freshwater mussel habitats across Missouri, USA

Point-source sedimentation, such as spills from construction-related activities, can introduce substantial sediments into streams in the short term, potentially leading to mussel burial. To estimate downstream areas where freshwater mussels might face threats from sediment burial within the mussel habitats of Missouri streams and rivers, we examined 49 reaches where both field measurements and gaging data are available. We established empirical relationships for three flow classes to represent general flow conditions of all reaches. Using these hydraulic data, we employed a Lagrangian particle tracking model to simulate sediment transport under each condition, employing two sediment size ranges covering very fine sands to small gravels, resulting in 72 simulated scenarios. The model results indicate that sediments with diameters exceeding a critical value, ranging from 0.041 to 1.975 mm for varying velocities (ranging from 0.124 to 2.191 m/s) and depths (ranging from 1 to 12 m), settle in downstream locations. Potential settling sites span from tens to hundreds of meters downstream. The mode, median, and mean of sediment distribution generally fall within the range of 10–200 m based on particle count, while these values typically range from 1 to 100 m based on sediment mass.

Missouri↗

USGS2025

Using the D-Claw software package to model lahars in the Middle Fork Nooksack River drainage and beyond, Mount Baker, Washington

Lahars, or volcanic mudflows, are the most hazardous eruption-related phenomena that will affect communities living along rivers that originate on Mount Baker. In the past 15,000 years, the largest lahars from Mount Baker have affected the Middle Fork Nooksack River drainage and beyond. Here we use the physics-based D-Claw software package to model nine lahar scenarios that are initiated as water-saturated landslides between Sherman Crater and the Roman Wall on the Mount Baker edifice and flow down the Middle Fork Nooksack River. The scenarios range in volume from 1 to 260 million cubic meters and have an initial hydraulic permeability from 10 −12 to 10 −10 meters squared. Model output includes data such as flow depth, velocity, runout distance, area inundated, arrival time, and sediment concentration as well as information that allows scientists to calculate other important hydrologic characteristics such as lahar discharge. These data are important to officials who have the responsibility to plan for, or take mitigation measures against, future Mount Baker lahars. To check the validity of the D-Claw results, we compare the scenarios to known geologic information. We also compare D-Claw results with empirical models that have been used in the past to determine potential inundation areas, runout distances, and arrival times. These comparisons highlight similarities and differences between empirical and physics-based models. We also present D-Claw scenario-based animations to help scientists, officials, and lay people alike to visualize how future lahars could affect communities.

Washington↗

USGS2025

Social sensing a volcanic eruption: Application to Kīlauea, 2018

Protecting lives and livelihoods during volcanic eruptions is the key challenge in volcanology, conducted primarily by volcano monitoring and emergency management organisations, but it is complicated by scarce knowledge of how communities respond in times of crisis. Social sensing is a rapidly developing practice that can be adapted for volcanology. Here we use social sensing of Twitter (currently known as X) posts to track changes in social action and reaction throughout the 2018 eruption of Kīlauea on the island of Hawai`i. The volume of relevant posts very rapidly increases in early May, coincident with the beginning of the eruption; automated sentiment analysis shows a simultaneous shift towards more negative emotions being expressed in post text. Substantial negative trends in sentiment are evident in reaction to high-impact events, including the destruction of a popular residential area and injuries sustained by tourists viewing the eruption. Topics of local Twitter conversation reveal societal actions, including the sharing of hazard warnings, mitigation actions, and aid announcements. Temporal trends in societal actions reflect patterns in volcanic activity (e.g. the peak and waning of eruptive activity), civil protection actions (e.g. risk mitigation actions and the communication of official warnings), and socioeconomic pressures (e.g. the destruction of homes). Local tweets detailing eruption damage and disruption display a similar temporal trend to independent estimates of the number of buildings in contact with lava. We show how hazard and risk information is discussed and reacted to on Twitter, which helps inform our understanding of community response actions and aids situational awareness, and outline how our approach could be adapted for use in real time.

Hawaii↗

USGS2025

Antigone canadensis (Sandhill Crane) foraging patterns influenced by crop type, roost distance, and tillage intensity during spring and autumn migration at a primary stopover area

The San Luis Valley in Colorado, USA, an agriculturally dominated stopover area, is used by the Rocky Mountain population of Antigone canadensis tabida (Greater Sandhill Crane) and some midcontinental individuals of A. c. canadensis (Lesser Sandhill Crane) during migration. While the numbers of both subspecies are stable, the effects of continued water scarcity and declines in grain output on the energetics of cranes in the San Luis Valley are unclear. We conducted roadside counts of A. c. tabida and A. c. canadensis on agricultural fields to determine the effects of crop type, roost distance, and tillage intensity on their selection and abundance on crop fields. Antigone canadensis varied in their use of the San Luis Valley for foraging. In autumn, both subspecies selected barley and other grains over other crop types. In spring, cranes preferred to forage in barley fields, and selection declined as distance to roosts increased. Both subspecies also selected barley fields that were lightly or not tilled. We modeled covariates on abundance for A. c. tabida only and found that more cranes were found close to roosts early in the season in autumn. As the season progressed, the number of A. c. tabida increased as roost distance increased. In spring, abundance was influenced by an interaction between time and crop, with the highest numbers found on barley and pasture around mid-March. Our results suggest that A. canadensis may switch to other crop types as resources are depleted near roosts but appear to prefer to fly farther for grains. Grains that are left idle or moderately tilled and are located near roosts will help ensure A. canadensis are able to maintain adequate nutrient reserves at agriculturally dominated stopover areas during migration.

Colorado↗

USGS2025

Small waterbodies of large conservation concern: Towards an integrated approach to more accurately measuring surface water dynamics

Millions of small waterbodies are dispersed throughout the middle of the North American continent, and billions of dollars have been invested to conserve, restore, and manage these waterbodies in the 20th and 21st centuries. Small waterbody conservation has been supported by different stakeholders aiming at improving water quality, enhancing floodwater storage, and supporting migratory bird breeding habitat. Conservation agencies are using hydrological and biological monitoring, modeling, and mapping to adaptively manage small waterbodies in the face of stressors such as invasive species and climate change. As remote sensing estimates of small waterbody surface water extent have become easier to access, understanding the capabilities and limitations of using remote sensing, especially in areas lacking surface water monitoring, is important for conservation decision making. Here, we used in situ monitoring and process-based hydrological modeling to explore remote sensing accuracy, especially related to waterbody size, emergent aquatic vegetation cover, and climatic conditions. Overall, we found that the accuracy of satellite and aerial imagery surface water mapping approaches vastly decreased for waterbodies smaller than 2 ha. We also found emergent vegetation could be masking surface water in waterbodies larger than 2 ha and that accuracy of some remote sensing estimates may decrease during wetter climatic periods. These results indicate that sensors commonly used for surface water applications alone may not be able to accurately detect small waterbody surface water, which supports the need for combining monitoring and modeling to understand how small waterbodies may respond to future changes in climate and land use.

Minnesota↗

USGS2025

Nature-based solutions extend the lifespan of a regional levee system under climate change

Nature-based solutions are receiving increasing attention as a cost-effective climate adaptation strategy. Horizontal levees are nature-based adaptation solutions that include a sloping wetland habitat buffer fronting a levee. They can offer a hybrid solution to reinforce traditional levees in estuarine areas—plants on the horizontal levee can provide wave attenuation benefits as well as habitat benefits, but how the design of horizontal levees influences risk of levee failure remains unquantified. We use a hydrodynamic model, XBeach non-hydrostatic (XB-NH), to assess the stability and sustainability of existing levees and determine how hybrid nature-based climate adaptation measures can reduce the risk of overtopping on levees in San Francisco Bay. We compare overtopping rates in the existing levee system and in a variety of nature-based adaptation scenarios using a range of widths and slopes of horizontal levees to assess how horizontal levees perform in reducing risk of flooding, both with present day conditions and sea level rise. We show that climate change will challenge existing levee flood defenses in San Francisco Bay and increase the risk of overtopping, and that the nature-based solution of horizontal levees can meaningfully reduce risk of overtopping while simultaneously supporting marsh habitat. Flood risk reduction and habitat provision are both maximized with more gradually sloping and wider horizontal levee designs. Results show that the risk of overtopping can be reduced by up to 30% with horizontal levees. This analysis provides insight into horizontal levee design considerations and a methodological approach to adapt levees to prepare for climate change in urban wave-exposed estuaries. We show that horizontal levees can support preparation for the projected impacts of sea level rise (SLR) while simultaneously providing new intertidal wetland habitat.

California↗

USGS2025

Status of water-level altitudes and long-term and short-term water-level changes in the Chicot and Evangeline (undifferentiated) and Jasper aquifers, greater Houston area, Texas, 2024

Since the early 1900s, groundwater withdrawn from the primary aquifers that compose the Gulf Coast aquifer system—the Chicot, Evangeline, and Jasper aquifers—has been an important source of water in the greater Houston area, Texas. This report, prepared by the U.S. Geological Survey in cooperation with the Harris-Galveston Subsidence District, City of Houston, Fort Bend Subsidence District, Lone Star Groundwater Conservation District, and Brazoria County Groundwater Conservation District, is one in an annual series of reports depicting the status of water-level altitudes and water-level changes in these aquifers in the greater Houston area. In this report, the Chicot and Evangeline aquifers are treated as a single aquifer for the purposes of providing annual assessments of regional-scale water-level altitudes and water-level changes over time. In 2024, shaded depictions of estimated water-level altitudes for the Chicot and Evangeline aquifers (undifferentiated) ranged from about 301 feet (ft) below the North American Vertical Datum of 1988 (NAVD 88) to about 184 ft above NAVD 88. The largest decline in water-level altitudes depicted by the 1977–2024 long-term water-level-change map was in south-central Montgomery County. In comparison, the 1990–2024 long-term water-level-change map depicts the largest declines in water-level altitudes in an area northwest of The Woodlands and in an area of northern Waller County. The largest rise in water-level altitudes for 1977–2024 is depicted in an area of east-central Harris County, whereas the largest rise in water-level altitudes for 1990–2024 is depicted in an area of central Harris County. The 5-year short-term water-level-change map depicts the largest declines in several parts of the study area, but these declines are concentrated primarily in northern Fort Bend County, southwestern Harris County, and south-central Montgomery County. The largest rise for 2019–24 is depicted at a well in northern Fort Bend County. The 1-year short-term water-level-change map depicts the largest declines at a well in northern Fort Bend County and a well in west-central Harris County. The largest rise for 2023–24 is depicted at a well in east-central Fort Bend County. In 2024, shaded depictions of estimated water-level altitudes for the Jasper aquifer ranged from about 255 ft below NAVD 88 to about 321 ft above NAVD 88. The 2000–24 long-term water-level-change map depicts the largest water-level decline in an area of central San Jacinto County; the largest rise is depicted in an area of central Grimes County. The 5-year short-term water-level-change map depicts the largest declines across parts of central and southern Montgomery County and at one well in north-central Harris County. The largest rise for 2019–24 is depicted at a well centered on the Montgomery-Grimes County line. The 1-year short-term water-level-change map depicts the largest declines at two wells in south-central Montgomery County and one well in northwestern Montgomery County on the west side of Lake Conroe. The largest rises during 2023–24 are depicted at one well in northwestern Montgomery County and one well in south-central Montgomery County.

Texas↗

USGS2025

Variability in hydrologic response to wildfire between snow zones in forested headwaters

Rising temperatures and shifting fire regimes in the western United States are pushing fires upslope into areas of deep winter snowpack, where we have little knowledge of the likely hydrologic impacts of wildfire. We quantified differences in the timing and magnitude of stormflow responses to summer rainstorms among six catchments of varying levels of burn severity and seasonal snowpack cover for years 1–3 after the 2020 Cameron Peak fire. Our objectives were to (1) examine whether responsiveness, magnitude, and timing of stormflow responses to rainfall vary between burned and unburned catchments and between snow zones, and (2) identify the factors that affect these responses. We evaluated whether differences in storm hydrograph peak flow, total flow, stage rise, and lag to peak time differed by snow zone and burn category using generalised linear models. Additional predictors in these models are the maximum 60-min rainfall intensity for each storm, the cumulative potential water deficit prior to the storm, and the year post-fire. These models showed that the high snow zone (HSZ) has higher total stormflow than the low snow zone (LSZ), likely due to the higher soil moisture content in that area. In both snow zones, the biggest driver of the magnitude of the stormflow response was MI 60 . Burn category did not have a clear impact on stormflow response in the HSZ, but it did impact stage rise at the severely burned catchment in the LSZ. This was the only site that had widespread overland flow post-fire. These results demonstrate that the stormflow responses to fire vary between snow zones, indicating a need to account for elevation and snow persistence in post-fire risk assessments.

Colorado↗

USGS2025

Marginalizing time in habitat selection and species distribution models improves inference

Aim Recent methodological advances for studying how animals move and use space with telemetry data have focused on fine-scale, more mechanistic inference. However, in many cases, researchers and managers remain interested in larger scale questions regarding species distribution and habitat use across study areas, landscapes, or seasonal ranges. Point processes offer a unified framework for many methods applied in studies of species distribution and resource selection; however, challenges remain in terms of dealing with temporal autocorrelation common in many types of telemetry data collected from animal locations. Innovation Space–time point processes (STPPs) have a unique property, in that marginalising time offers a connection between individual animal movement and broader point processes, yet this property has seen little attention in both statistical and applied research. In this paper, we first present some of the details of this marginalisation property and methods for applying marginalised STPPs (mSTTPs) to autocorrelated telemetry data and then apply a mSTTP in a case study on the summer space use and habitat selection of female caribou ( Rangifer tarandus ) in Denali National Park and Preserve, Alaska. Main Conclusions The case study demonstrated that an mSTPP approach can improve inference over other commonly used methods in terms of its ability to account for temporal autocorrelation and offers greater precision in parameter estimates and improved predictions of space use. As this method fits conveniently into the existing point process frameworks, it offers a practical solution to dealing with temporal autocorrelation inherent to many types of telemetry data when research questions center around broader scale patterns of animal habitat selection and space use.

Alaska↗

USGS2025

Ultrasonic deterrents provide no additional benefit over curtailment in reducing bat fatalities at an Ohio wind energy facility

Wind energy is important for achieving net-zero greenhouse gas emissions but also contributes to global bat mortality. Current strategies to minimize bat mortality due to collision with wind-turbine blades fall broadly into two categories: curtailment (limiting turbine operation during high-risk periods) and deterrence (discouraging bat activity near turbines). Recently, there has been interest in combining these strategies to achieve greater reductions in bat fatalities than either strategy might achieve in isolation. To investigate the effectiveness of combining curtailment with ultrasonic deterrent minimization strategies, we deployed six ultrasonic deterrents at nacelle height on 16 experimental turbines at Avangrid Renewables’ Blue Creek Wind Energy Facility. We rotated between four conditions (normal operations, curtailment only, deterrent only, curtailment and deterrent) randomly assigned to four wind turbines each night between 15 June and 3 October 2017. We found that bat mortality at wind turbines was independent of wind speed. The effectiveness of ultrasonic acoustic deterrents varied between high-frequency-calling species (eastern red bats) and low-frequency-calling species (hoary bats, silver-haired bats, and big brown bats). When deterrents were active, mortality was twice as high for eastern red bats compared to the control. Conversely, deterrents had a weak dampening effect on bat mortality for low-frequency species. We found no additive effects on mortality reduction for turbines operating both curtailment and deterrents compared to either approach in isolation. Our findings suggest that ultrasonic acoustic deterrents may not be effective for both high and low frequency echolocating bats. The increase in fatalities of eastern red bats is alarming and underscores the importance of considering site- and species-specific effects of minimization solutions.

Ohio↗

USGS2025

Leveraging detection uncertainty to estimate Renibacterium salmoninarum infection status among multiple tissues and assays

Effective disease surveillance relies on accurate pathogen testing and robust prevalence estimates. Diagnostic specificity (DSp), the probability that an uninfected animal tests negative, is high when false positives are low. Diagnostic sensitivity (DSe) is the probability an infected animal tests positive; higher DSe means fewer false negatives. However, sensitivity and false negatives are harder to estimate without a "gold standard", an assay that can detect between 90 - 100% of true positive infections. Occupancy estimation of infection prevalence offers one solution by allowing for imperfect detection of the pathogen. Testing potentially infected tissues multiple times allows for the use of a Bayesian multistate occupancy model to estimate the probability of pathogen infection in tissues [Formula: see text] and detection probabilities [Formula: see text] for different assays. Using [Formula: see text] and [Formula: see text] from the posterior distribution, the conditional probability of detecting the pathogen can be modeled, allowing for the calculation of DSe. Renibacterium salmoninarum is a bacterial pathogen causing bacterial kidney disease among salmonid species and was the model pathogen we used to train our model. The current testing standard for salmonids combines initial screening for antibodies using direct fluorescent antibody test (DFAT) with polymerase chain reaction (PCR) confirmation to detect R. salmoninarum. However, detection of R. salmoninarum still varies between species, tissues, and assays. Here, a multi-state occupancy model was used to estimate detection probability among individual and dual kidney/liver infections with DFAT and qPCR in fish with an unknown infection status. Both assays produced false negatives, but qPCR had fewer than DFAT and a higher DSe. Infection state was often misclassified, but multiple surveys per individual or combining tissues for testing improved DSe for both assays.

conterminous United States↗

USGS2025

A partner-driven decision support model to inform the reintroduction of bull trout

Assessments of species reintroductions involve a series of complex decisions that include human perspectives and ecological contexts. Here, we present a reintroduction assessment involving bull trout ( Salvelinus confluentus ) using a structured decision-making process. We approached this assessment by engaging partners representing public utilities, government agencies, and Tribes with shared interests in a potential reintroduction. These individuals identified objectives, decision alternatives, and ecological scenarios that were incorporated into a co-produced simulation-based model of potential reintroduction outcomes. The model included mathematical representations of habitat availability, life history expression, and assumptions regarding constraints on potential bull trout populations. Within each recipient stream, partners chose to explore a wide range of decision alternatives and simulated scenarios affecting reintroduction success. Results suggested that 1) reintroductions using eggs or adults were most optimal, 2) adding more individuals resulted in diminishing returns, 3) access to migratory habitat could improve success, and 4) the diversity of opportunities for life history expression led to improved reintroduction opportunities. In addition, modeled scenarios indicated some recipient streams consistently produced lower abundance of reintroduced bull trout. This work contributes a novel example to a growing portfolio of reintroduction assessments that may inform future conservation for bull trout and many other species facing similar challenges.

Washington↗