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At least 1,297 records · Page 72Linked to original sources
USGS2019

Using environmental DNA (eDNA) to assess the presence of cavefish and cave crayfish populations in caves of the Ozark Highlands

Many cavefishes and cave crayfishes are considered of conservation concern; however, sampling these species is inherently difficult given their occupied environments. The goal of our project was to verify the presence of select karst organisms while developing the foundation for sampling approaches that might be useful to conservation and management agencies. Our project objectives were to develop assays to amplify deoxyribonucleic acid (DNA) from several species of Ozark cavefishes and cave crayfishes and complete an initial surveillance of locations across the Ozark Highlands using environmental DNA (eDNA). Using DNA either provided by agency cooperators or that we extracted from tissue samples, we PCR amplified and then sequenced the Cytochrome Oxidase 1 (CO1) gene for cave crayfishes and the NADH Dehydrogenase Subunit 2 (ND2) gene for cavefishes. We developed species-specific primers and probes for five cave crayfishes and two cavefishes. From February 2017 to May 2017, we sampled 1–5 sampling units from 42 caves, wells, and springs (i.e., sites) using eDNA and traditional visual surveys. We measured physicochemical parameters at each sampling unit to estimate detection probability associated with both techniques. We also calculated two occupancy covariates for each site using geospatial data. We successfully amplified Troglichthys rosae DNA from the environment and detected DNA representing this species at 24 of 40 sites. At 16 of the sites where we detected T. rosae DNA, we did not visually observe the species. Although our assay for Typlichthys eigenmanni successfully amplified the target DNA from the environment, it also resulted in false absences where the species was visually confirmed. Using eDNA to detect cave crayfishes was much more difficult. The assay for Cambarus subterraneus did not work for eDNA samples and we were unable to pick up DNA from the environment, even at locations where it was visually confirmed. Alternatively, the eDNA surveys worked well for C. tartarus and we were able to amplify DNA at every site where it was visually observed. Our assay for C. aculabrum was based on a single sample obtained from GenBank, and did not amplify eDNA from field samples. Lastly, our eDNA results from samples in the known range of Orconectes stygocaneyi suggested the species may be found at an additional cave. Detection using eDNA based on our O. stygocaneyi assay was likely low because it was designed from a pseudogene; however, positive eDNA samples were sequenced to confirm species-specific DNA. Detection probability of both cavefishes and cave crayfishes varied by survey technique and was influenced by water volume, water clarity, water velocity, and substrate. Detection of cavefishes and cave crayfishes via visual surveys decreased when water volume increased, whereas detection using eDNA increased with greater water volume. Detection between taxa using either sample method was highest in habitats classified by fine substrates, except for eDNA detection of crayfishes which was greatest in coarse substrates. Detection of cavefishes increased with water clarity, but detection of cave crayfishes increased with turbidity. Detection probability of both cavefishes and crayfishes using eDNA increased slightly with water velocity, but decreased with visual surveys as water velocity increased. Occupancy by both taxa was positively related to particular geologic series. Crayfish occupancy was negatively related to fine-scale anthropogenic disturbance (i.e., 500-m buffer around the site), whereas crayfish showed no relationship with disturbance. Our results suggest possible range extensions, provide insights to factors driving detection using both sample techniques, and suggest areas where recharge zones may be shared among caves. Future efforts focused on a comprehensive evaluation of genetic diversity among cave crayfishes to improve assay design could improve detection and the applicability of eDNA as a supplemental and non-invasive sampling approach.

Cooperator Science Series↗
USGS2026

An automated geographic information system-based hydraulic modeling tool for developing preliminary culvert designs for stream crossings in Massachusetts

Introduction Currently (2026), many of the about 25,000 roadway crossing structures over rivers and streams in Massachusetts are undersized. Undersized culverts and bridges can be detrimental to fish and wildlife movement, habitat continuity, and the health of aquatic organisms. Undersized culverts also can lack the resiliency needed to withstand large floods, which could be worsened by potential increases in flood magnitude and frequency due to climate change. Improving culvert and bridge designs for stream crossing projects may improve aquatic organism passage, stream continuity, and resiliency during future floods by decreasing upstream overbank flooding, road flooding and erosion, and degradation of aquatic habitat. The U.S. Geological Survey (USGS), Massachusetts Department of Environmental Protection (MassDEP), and University of Massachusetts Amherst began a series of cooperative studies in July 2019 to develop an automated geographic information system (GIS) hydraulic modeling tool for preliminary culvert designs for stream crossings. The USGS plans to provide preliminary culvert designs in the web-based StreamStats application, which enables municipalities and engineers to view potential designs and related information for stream crossing replacement projects in Massachusetts. This application can (a) provide information on hydrology, hydraulics, and ecological conditions at stream crossing sites, (b) provide users with potential culvert designs to improve aquatic organism passage and flood resiliency, and (c) assist MassDEP in implementing the Massachusetts Wetlands Protection Act regulations for stream crossing projects.

Massachusetts↗
USGS1979

Chemical and biological quality of selected lakes in Ohio, 1976 and 1977

Twenty-eight Ohio lakes (14 per year) were sampled by the U.S. Geological Survey and Ohio Environmental Protection Agency for the water-quality characteristics during the spring and summer of 1976 and 1977. Data items included: profiles of temperature, dissolved oxygen, pH, and specific conductance; physical, biological, nutrient, and organic characteristics; major and minor constituents; and physical and chemical data associated with major inflows. Light penetration (secchi disk) was greatest (21 feet) in Mogadore Reservoir and least (0.8 foot) in Stonelick Lake. Seasonal thermal gradients developed in most lakes greater than 17 feet in depth. Dissolved-oxygen saturation ranged from 220 percent in Summit Lake to zero percent in the bottom waters of all lakes having stable thermal gradients. Five-day BOD ranged from 0.3 milligrams per liter im Michael J. Kirwan Reservoir to more than 17 milligrams per liter in Nimisilia Reservoir. Anaerobic zones were frequently characterized by hydrogen sulfide and high concentrations of ammonia. All lakes had moderately hard to very hard waters. Calcium, bicarbonate, and sulfate were the principal constituents. Specific conductance ranged from 130 micromhos (Lake Logan) to 1250 micromhos (Summit Lake). Because of nutrient uptake and recycling, significant chemical and physical differences developed in different thermal strata. Pesticide residues and trace elements were not above the limits recommended by the Ohio Environmental Protection Agency. All counts of fecal colifrom bacteria were within State standards. Blue-green algae (Cyanophyta) dominated the phytoplankton communities of 18 lakes in spring and 26 lakes in summer. Algal counts from euphotic-zone composite samples ranged from 180 cells per milliliter in Killdeer Reservoir to 3,400,000 cells per milliliter in Kiser Lake. Maximum algal counts were greater than 100,000 cells per milliliter in 19 lakes. Streams ate a major source of macronutrients in Ohio lakes. The estimated discharge-weighted mean concentration for nitrite and total phosphorus in 62 inflow samples was 1.22 milligrams per liter as N and 0.12 milligrams per liter as P.

Ohio↗
USGS2025

Geothermal potential of orphan oil and gas wells

The United States is estimated to have hundreds of thousands of orphan oil and gas wells. Orphan wells are abandoned wells that are both unremediated and have no responsible operator. While traditionally considered environmental and economic liabilities, orphan oil and gas wells may offer new opportunities in sustainable geothermal energy development. This study evaluates the potential of repurposing orphan wells for geothermal energy production. We analyzed more than 1.4 million bottom-hole temperature (BHT) records from oil and gas well logs to create corrected temperature-depth profiles in a grid across the United States. Total depth values, where available, in documented orphan wells from a U.S. Geological Survey (USGS) database were then correlated to these temperature-depth profiles to estimate a corrected BHT for each orphan well. The orphan wells were then categorized as having low (<90°C), moderate (90–150°C), and high (>150°C) geothermal potential, identifying them as wells in the U.S. that could be used to access geothermal resources. In addition, repurposing these wells could contribute to broader environmental and economic goals, including well remediation, rogue methane emissions reduction, and energy production. This study provides a framework for integrating inactive well inventories with geothermal resource assessments and further highlights the potential for orphan wells to play a transformative role in expanding geothermal energy capacity in the United States.

contiguous United States↗
USGS2024

Environmental DNA (eDNA) surveillance of the federally threatened Slender Chub (Erimystax cahni) in the Clinch River and Powell River

The slender chub ( Erimystax cahni ) is a federally threatened fish native to and geographically restricted to eastern North America. More specifically, the Powell, Clinch, and lower Holston Rivers in Tennessee were historical collection areas. Habitat degradation from multiple sources, including surface mining, agriculture, dams, and urbanization, is associated with the decline of this species - an obligate inhabitant of gravel shoals in large rivers. As of 1964, only 15 voucher specimens were known and no living specimens were documented for decades. A federal recovery plan and Species Status Assessment were developed to determine if slender chub still exists and could be restored. Given the lack of recent observations using conventional sampling to search for its presence, we used environmental DNA sampling to determine their potential presence. Our specific objectives were to (1) develop a quantitative polymerase chain reaction (qPCR) assay aimed at species-specific detection and (2) sample historically known areas of collection. We sampled 43 sites in the Clinch and Powell Rivers. For the first time in almost two decades, we provide evidence for the continued existence of a putatively extinct species. We detected evidence of E. cahni in both the Clinch and Powell Rivers, but only at a few sites. We cannot confirm the presence of E. cahni , and positive eDNA matches could be attributed to amplification from a hybrid. Our results do indicate slender chub DNA perseveres in the Clinch and Powell Rivers and can inform resource agencies of localities to pursue on-the-ground searches for the slender chub with conventional methods (e.g., snorkeling) and potential restoration and recovery sites.

Tennessee, Virginia↗
USGS2018

Demographic response of Louisiana Waterthrush, a stream obligate songbird of conservation concern, to shale gas development

Shale gas development continues to outpace the implementation of best management practices for wildlife affected by development. We examined demographic responses of the Louisiana Waterthrush ( Parkesia motacilla ) to shale gas development during 2009–2011 and 2013–2015 in a predominantly forested landscape in West Virginia, USA. Forest cover across the study area decreased from 95% in 2008 to 91% in 2015, while the area affected by shale gas development increased from 0.4% to 3.9%. We quantified nest survival and productivity, a source–sink threshold, riparian habitat quality, territory density, and territory length by monitoring 58.1 km of forested headwater streams ( n = 14 streams). Across years, we saw annual variability in nest survival, with a general declining trend over time. Of 11 a priori models tested to explain nest survival ( n = 280 nests), 4 models that included temporal, habitat, and shale gas covariates were supported, and 2 of these models accounted for most of the variation in daily nest survival rate. After accounting for temporal effects (rainfall, nest age, and time within season), shale gas development had negative effects on nest survival. Population-level nest productivity declined and individual productivity was lower in areas disturbed by shale gas development than in undisturbed areas, and a source–sink threshold suggested that disturbed areas were more at risk of being sink habitat. Riparian habitat quality scores, as measured by a U.S. Environmental Protection Agency index and a waterthrush-specific habitat suitability index, differed by year and were negatively related to the amount of each territory disturbed by shale gas development. Territory density was not related to the amount of shale gas disturbance, but decreased over time as territory lengths increased. Overall, our results suggest a decline in waterthrush site quality as shale gas development increases, despite relatively small site-wide forest loss.

West Virginia↗
USGS2017

Meteorological and environmental variables affect flight behaviour and decision-making of an obligate soaring bird, the California Condor Gymnogyps californianus

The movements of animals are limited by evolutionary constraints and ecological processes and are strongly influenced by the medium through which they travel. For flying animals, variation in atmospheric conditions is critically influential in movement. Obligate soaring birds depend on external sources of updraft more than do other flying species, as without that updraft they are unable to sustain flight for extended periods. These species are therefore good models for understanding how the environment can influence decisions about movement. We used meteorological and topographic variables to understand the environmental influences on the decision to engage in flight by obligate soaring and critically endangered California Condors Gymnogyps californianus . Condors were more likely to fly, soared at higher altitudes and flew over smoother terrain when weather conditions promoted either thermal or orographic updrafts, for example when turbulence and solar radiation were higher and when winds from the east and north were stronger. However, increased atmospheric stability, which is inconsistent with thermal development but may be associated with orographic updrafts, was correlated with a somewhat higher probability of being in flight at lower altitudes and over rougher terrain. The close and previously undescribed linkages between Condor flight and conditions that support development of thermal and orographic updrafts provide important insight into the behaviour of obligate soaring birds and into the environmental parameters that may define the currently expanding distribution of Condors within and outside the state of California.

California↗
USGS2017

Climate change may restrict dryland forest regeneration in the 21st century

The persistence and geographic expansion of dryland forests in the 21st century will be influenced by how climate change supports the demographic processes associated with tree regeneration. Yet, the way that climate change may alter regeneration is unclear. We developed a quantitative framework that estimates forest regeneration potential (RP) as a function of key environmental conditions for ponderosa pine, a key dryland forest species. We integrated meteorological data and climate projections for 47 ponderosa pine forest sites across the western United States, and evaluated RP using an ecosystem water balance model. Our primary goal was to contrast conditions supporting regeneration among historical, mid-21st century and late-21st century time frames. Future climatic conditions supported 50% higher RP in 2020–2059 relative to 1910–2014. As temperatures increased more substantially in 2060–2099, seedling survival decreased, RP declined by 50%, and the frequency of years with very low RP increased from 25% to 58%. Thus, climate change may initially support higher RP and increase the likelihood of successful regeneration events, yet will ultimately reduce average RP and the frequency of years with moderate climate support of regeneration. Our results suggest that climate change alone may begin to restrict the persistence and expansion of dryland forests by limiting seedling survival in the late 21st century.

Ecology↗
USGS2018

Hierarchical multi-population viability analysis

Population viability analysis (PVA) uses concepts from theoretical ecology to provide a powerful tool for quantitative estimates of population dynamics and extinction risks. However, conventional statistical PVA requires long-term data from every population of interest, whereas many species of concern exist in multiple isolated populations that are only monitored occasionally. We present a hierarchical multi-population viability analysis model that increases inference power from sparse data by sharing information among populations to assess extinction risks while accounting for incomplete detection and sampling biases with explicit observation and sampling sub-models. We present a case study in which we customized this model for historical population monitoring data (1985–2015) from federally threatened Lahontan cutthroat trout populations in the Great Basin, USA. Data were counts of fish captured during backpack electrofishing surveys from locations associated with 155 isolated populations. Some surveys (25%) included multi-pass removal sampling, which provided valuable information about capture efficiency. GIS and remote sensing were used to estimate August stream temperatures, peak flows, and riparian vegetation condition in each population each year. Field data were used to derive an annual index of nonnative trout densities. Results indicated that population growth rates were higher in colder streams and that nonnative trout reduced carrying capacities of native trout. Extinction risks increased with more environmental stochasticity and were also related to population extent, water temperatures, and nonnative densities. We developed a graphical user interface to interact with the fitted model results and to simulate future habitat scenarios and management actions to assess their influence on extinction risks in each population. Hierarchical multi-population viability analysis bridges the gap between site-level field observations and population-level processes, making effective use of existing datasets to support management decisions with robust estimates of population dynamics, extinction risks, and uncertainties.

Ecology↗
USGS2015

Adaptive management of social-ecological systems: The path forward

Adaptive management remains at the forefront of environmental management nearly 40 years after its original conception, largely because we have yet to develop other methodologies that offer the same promise. Despite the criticisms of adaptive management and the numerous failed attempts to implement it, adaptive management has yet to be replaced with a better alternative. The concept persists because it is simple, allows action despite uncertainty, and fosters learning. Moving forward, adaptive management of social-ecological systems provides policymakers, managers and scientists a powerful tool for managing for resilience in the face of uncertainty.

Book chapter↗
USGS2013

Perception, experience, and indigenous knowledge of climate change and variability: the case of Accra, a sub-Saharan African city

Several recent international assessments have concluded that climate change has the potential to reverse the modest economic gains achieved in many developing countries over the past decade. The phenomenon of climate change threatens to worsen poverty or burden populations with additional hardships, especially in poor societies with weak infrastructure and economic well-being. The importance of the perceptions, experiences, and knowledge of indigenous peoples has gained prominence in discussions of climate change and adaptation in developing countries and among international development organizations. Efforts to evaluate the role of indigenous knowledge in adaptation planning, however, have largely focused on rural people and their agricultural livelihoods. This paper presents the results of a study that examines perceptions, experiences, and indigenous knowledge relating to climate change and variability in three communities of metropolitan Accra, which is the capital of Ghana. The study design is based on a three-part conceptual framework and interview process involving risk mapping, mental models, and individual stressor cognition. Most of the residents interviewed in the three communities of urban Accra attributed climate change to the combination of deforestation and the burning of firewood and rubbish. None of the residents associated climate change with fossil fuel emissions from developed countries. Numerous potential adaptation strategies were suggested by the residents, many of which have been used effectively during past drought and flood events. Results suggest that ethnic residential clustering as well as strong community bonds in metropolitan Accra have allowed various groups and long-settled communities to engage in the sharing and transmission of knowledge of weather patterns and trends. Understanding and building upon indigenous knowledge may enhance the design, acceptance, and implementation of climate change adaptation strategies in Accra and urban regions of other developing nations.

Accra↗
USGS2026

The impacts of cover crop biomass on satellite-based detectability of cover crops in Maryland

Cover crop adoption in the U.S. has increased over the past decades, increasing the need to quantify their performance and environmental benefits. While remote sensing (RS)-based approaches for detecting cover crop presence have been developed, there has been limited research on how cover crops with varied biomass and management practices influence detectability. Using unique field-level cover crop presence and biomass datasets in Maryland, U.S., we investigated how RS-based detectability changes for cover crops with varied aboveground biomass, planting, and termination dates. Specifically, we proposed a time-integrated satellite-based greenness feature from Harmonized Landsat-8 and Sentinel-2 (HLS) time series from 2017 to 2021 to estimate biomass of cover crops and evaluated their detectability using a phenology-based cover crop detection framework. The impacts of cover crop planting and termination dates on cover crop biomass were also analyzed. Our results demonstrated that Normalized Difference Vegetation Index (NDVI) estimated biomass with higher accuracy compared to other vegetation indices, and the time-integrated model estimated biomass with higher accuracy than the single-date “snapshot” linear model (R2 from 0.53 to 0.66 and RMSE from 922 kg/ha to 747 kg/ha). While the snapshot models were species sensitive, the time-integrated models showed strong robustness across different species. Detectability increased with cover crop biomass, as detected cover crops averaged 963.3 ±719.5 kg/ha compared to 297.2 ± 209.0 kg/ha for non-detected cover crops. Detection accuracy reached 96.1% for fields exceeding 500 kg/ha, compared with an overall accuracy of 62.7%. Earlier planting and later termination increased biomass and detectability, with biomass rising by 4.14 kg/ha/day (p < 0.01). This study demonstrates how management practices affect cover crop biomass and detectability via satellite time series and provides insights that can inform management of cover crops and monitoring of their effects on agroecosystems.

Maryland↗
USGS2017

Seasonal trends in eDNA detection and occupancy of bigheaded carps

Bigheaded carps, which include silver and bighead carp, are threatening to invade the Great Lakes. These species vary seasonally in distribution and abundance due to environmental conditions such as precipitation and temperature. Monitoring this seasonal movement is important for management to control the population size and spread of the species. We examined if environmental DNA (eDNA) approaches could detect seasonal changes of these species. To do this, we developed a novel genetic marker that was able to both detect and differentiate bighead and silver carp DNA. We used the marker, combined with a novel occupancy model, to study the occurrence of bigheaded carps at 3 sites on the Wabash River over the course of a year. We studied the Wabash River because of concerns that carps may be able to use the system to invade the Great Lakes via a now closed (ca. 2017) connection at Eagle Marsh between the Wabash River's watershed and the Great Lakes' watershed. We found seasonal trends in the probability of detection and occupancy that varied across sites. These findings demonstrate that eDNA methods can detect seasonal changes in bigheaded carps densities and suggest that the amount of eDNA present changes seasonally. The site that was farthest upstream and had the lowest carp densities exhibited the strongest seasonal trends for both detection probabilities and sample occupancy probabilities. Furthermore, other observations suggest that carps seasonally leave this site, and we were able to detect this with our eDNA approach.

Journal of Great Lakes Research↗
USGS2013

Appraising options to reduce shallow groundwater tables and enhance flow conditions over regional scales in an irrigated alluvial aquifer system

Some of the world’s key agricultural production systems face big challenges to both water quantity and quality due to shallow groundwater that results from long-term intensive irrigation, namely waterlogging and salinity, water losses, and environmental problems. This paper focuses on water quantity issues, presenting finite-difference groundwater models developed to describe shallow water table levels, non-beneficial groundwater consumptive use, and return flows to streams across two regions within an irrigated alluvial river valley in southeastern Colorado, USA. The models are calibrated and applied to simulate current baseline conditions in the alluvial aquifer system and to examine actions for potentially improving these conditions. The models provide a detailed description of regional-scale subsurface unsaturated and saturated flow processes, thereby enabling detailed spatiotemporal description of groundwater levels, recharge to infiltration ratios, partitioning of ET originating from the unsaturated and saturated zones, and groundwater flows, among other variables. Hybrid automated and manual calibration of the models is achieved using extensive observations of groundwater hydraulic head, groundwater return flow to streams, aquifer stratigraphy, canal seepage, total evapotranspiration, the portion of evapotranspiration supplied by upflux from the shallow water table, and irrigation flows. Baseline results from the two regional-scale models are compared to model predictions under variations of four alternative management schemes: (1) reduced seepage from earthen canals, (2) reduced irrigation applications, (3) rotational lease fallowing (irrigation water leased to municipalities, resulting in temporary dry-up of fields), and (4) combinations of these. The potential for increasing the average water table depth by up to 1.1 and 0.7 m in the two respective modeled regions, thereby reducing the threat of waterlogging and lowering non-beneficial consumptive use from adjacent fallow and naturally-vegetated lands, is demonstrated for the alternative management intervention scenarios considered. Net annual average savings of up to about 9.9 million m 3 (8000 ac ft) and 2.3 million m 3 (1900 ac ft) of non-beneficial groundwater consumptive use is demonstrated for the study periods in each of the two respective study regions. Alternative water management interventions achieve varying degrees of benefits in each of the two regions, suggesting a need to adopt region-specific interventions and avoid a ‘one-size-fits-all’ approach. Impacts of the considered interventions on return flows to the river were predicted to be significant, highlighting the need for flow augmentation to comply with an interstate river compact and portending beneficial impacts on solute loading.

Colorado↗
USGS2020

Comparison of SELDM simulated total-phosphorus concentrations with ecological impervious-area criteria

Ecological studies indicate that impervious cover (IC) greater than approximately 5%–20% may have adverse effects on receiving-stream ecology. It is difficult to separate the effects of runoff quality from other effects of urbanization on receiving streams. This study presents the results of a numerical experiment to assess the effects of increasing IC on water quality using the Stochastic Empirical Loading and Dilution Model (SELDM). Hydrologic and physiographic variables representative of southern New England were used to simulate receiving water quality in a basin with IC ranging from 0.1% to 30%. Simulation results mirror the results of ecological studies; event mean concentrations (EMCs) of total phosphorus (TP) increase proportionally to the logarithms of imperviousness for a given risk percentile. Simulation results indicated that commonly used stormwater treatment methods may be insufficient for mitigating the effects of imperviousness. Therefore, disconnection, rather than treatment, may be needed to protect water quality, and efforts to preserve undeveloped stream basins may be more effective than efforts to remediate conditions in highly developed basins. Results also indicate that commonly used water-quality criteria may be too restrictive for stormwater because TP EMCs frequently exceed these criteria, even in minimally developed basins.

Journal of Environmental Engineering↗
USGS2016

A framework for assessing the feasibility of native fish conservation translocations: Applications to threatened bull trout

There is an urgent need to consider more aggressive and direct interventions for the conservation of freshwater fishes that are threatened by invasive species, habitat loss, and climate change. Conservation introduction (moving a species outside its indigenous range to other areas where conditions are predicted to be more suitable) is one type of translocation strategy that fisheries managers can use to establish new conservation populations in areas of refugia. To date, however, there are few examples of successful conservation-based introductions. Many attempts fail to establish new populations&mdash;in part because environmental factors that might influence success are inadequately evaluated before the translocation is implemented. We developed a framework to assess the feasibility of rescuing threatened fish populations through translocation into historically unoccupied stream and lake habitats. The suitability of potential introduction sites was evaluated based on four major components: the recipient habitat, recipient community, donor population, and future threats. Specific questions were then developed to evaluate each major component. The final assessment was based on a scoring system that addressed each question by using criteria developed from characteristics representative of highly suitable habitats and populations. This framework was used to evaluate the proposed within-drainage translocation of three Bull Trout Salvelinus confluentus populations in Glacier National Park, Montana. Our results indicated that within-drainage translocation is a feasible strategy for conserving locally adapted populations of Bull Trout through the creation of new areas of refugia in Glacier National Park. The framework provides a flexible platform that can help managers make informed decisions for moving threatened fishes into new areas of refugia for conservation and recovery programs.

North American Journal of Fisheries Management↗
USGS2015

Optimal population prediction of sandhill crane recruitment based on climate-mediated habitat limitations

Prediction is fundamental to scientific enquiry and application; however, ecologists tend to favour explanatory modelling. We discuss a predictive modelling framework to evaluate ecological hypotheses and to explore novel/unobserved environmental scenarios to assist conservation and management decision-makers. We apply this framework to develop an optimal predictive model for juvenile (<1 year old) sandhill crane Grus canadensis recruitment of the Rocky Mountain Population (RMP). We consider spatial climate predictors motivated by hypotheses of how drought across multiple time-scales and spring/summer weather affects recruitment. Our predictive modelling framework focuses on developing a single model that includes all relevant predictor variables, regardless of collinearity. This model is then optimized for prediction by controlling model complexity using a data-driven approach that marginalizes or removes irrelevant predictors from the model. Specifically, we highlight two approaches of statistical regularization, Bayesian least absolute shrinkage and selection operator (LASSO) and ridge regression. Our optimal predictive Bayesian LASSO and ridge regression models were similar and on average 37% superior in predictive accuracy to an explanatory modelling approach. Our predictive models confirmed a priori hypotheses that drought and cold summers negatively affect juvenile recruitment in the RMP. The effects of long-term drought can be alleviated by short-term wet spring–summer months; however, the alleviation of long-term drought has a much greater positive effect on juvenile recruitment. The number of freezing days and snowpack during the summer months can also negatively affect recruitment, while spring snowpack has a positive effect. Breeding habitat, mediated through climate, is a limiting factor on population growth of sandhill cranes in the RMP, which could become more limiting with a changing climate (i.e. increased drought). These effects are likely not unique to cranes. The alteration of hydrological patterns and water levels by drought may impact many migratory, wetland nesting birds in the Rocky Mountains and beyond. Generalizable predictive models (trained by out-of-sample fit and based on ecological hypotheses) are needed by conservation and management decision-makers. Statistical regularization improves predictions and provides a general framework for fitting models with a large number of predictors, even those with collinearity, to simultaneously identify an optimal predictive model while conducting rigorous Bayesian model selection. Our framework is important for understanding population dynamics under a changing climate and has direct applications for making harvest and habitat management decisions.

Journal of Animal Ecology↗
USGS2025

Metabarcoding analysis of arthropod pollinator diversity: A methodological comparison of eDNA derived from flowers and DNA derived from bulk samples of insects

Limitations of traditional insect sampling methods have motivated the development and optimisation of new non-lethal methods capable of quantifying diverse arthropod communities. Environmental DNA (eDNA) metabarcoding using arthropod-specific primers has recently been investigated as a novel way to characterise arthropod communities from the DNA they deposit on the surface of plants. This sampling method has had demonstrated success, but pollinators—especially bees—are oddly underrepresented in these studies. To evaluate this inconsistency, we investigated the limitations of eDNA metabarcoding for bees and other pollinators. We compared pollinator diversity derived from eDNA extracted from flowers and DNA extracted from pulverised bulk samples of insects collected from vane traps deployed at the same sites using three metabarcoding primers, two of which target arthropods generally (COI-Jusino and 16S-Marquina) and one that targets bumblebees ( Bombus spp., COI-Milam). Across methods, we detected 77 insect families from 9 orders. The COI-Jusino marker amplified the highest taxonomic diversity compared to 16S-Marquina and COI-Milam. More amplicon sequence variants (ASVs) were recovered from vane traps (blue: 1357, yellow: 1542) than flowers (245), but only 23% of families and 13% of genera were shared among methods, indicating that flowers and blue and yellow vane traps may each sample different parts of the available arthropod community. Of 29 flower samples with known bee visitations, only 10 samples had bee detections from eDNA, and incomplete reference databases hindered assignment to species. Although our study provides additional evidence for the usefulness of eDNA metabarcoding for characterising arthropod communities, significant challenges remain when using eDNA metabarcoding methods to identify and quantify pollinator communities, especially bees.

Molecular Ecology↗