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USGS2025

Turning trash into treasure: Leveraging discarded filters for national-scale aquatic eDNA biomonitoring

Monitoring biodiversity changes over large spatiotemporal scales is critical for effective ecosystem conservation and management. This study investigates the potential of environmental DNA (eDNA) metabarcoding to enhance national-scale biomonitoring of freshwater diversity by leveraging discarded filters associated with routine water quality sampling from the U.S. Geological Survey's (USGS) National Water Quality Network (NWQN). We tested 375 samples from 103 NWQN sites for eDNA of native and non-native fish and found that 52% of the filters yielded fish eDNA for a total of 70 fish species detections. Of the filters that had fish eDNA present, an average of 3.7 species were detected. Benchmarking these results to USGS's Aquatic Gap Analysis Project (AGAP)—which includes both field-verified observations along with predictive models derived from fish capture and landscape predictor datasets—we found that eDNA from these filters detected only a fraction of the observed and expected fish diversity for these sites. Our results indicate that these discarded filters may not be sufficient for eDNA sampling of fish communities and posit that alternative filter types more appropriate for eDNA sampling may yield more valuable biomonitoring data. Nevertheless, we tested the efficacy of two novel approaches to facilitate large-scale biomonitoring. Though these filters did not yield adequate fish eDNA, the AGAP database provides a useful method for ground truthing fish species presence. The potential of integrating eDNA sampling into existing monitoring frameworks, which, when paired with more optimal eDNA methods, could be a cost-effective strategy to enhance biodiversity monitoring at large scales.

Aquaculture, Fish and Fisheries↗

USGS2015

Arctic biodiversity: Increasing richness accompanies shrinking refugia for a cold-associated tundra fauna

As ancestral biodiversity responded dynamically to late-Quaternary climate changes, so are extant organisms responding to the warming trajectory of the Anthropocene. Ecological predictive modeling, statistical hypothesis tests, and genetic signatures of demographic change can provide a powerful integrated toolset for investigating these biodiversity responses to climate change, and relative resiliency across different communities. Within the biotic province of Beringia, we analyzed specimen localities and DNA sequences from 28 mammal species associated with boreal forest and Arctic tundra biomes to assess both historical distributional and evolutionary responses and then forecasted future changes based on statistical assessments of past and present trajectories, and quantified distributional and demographic changes in relation to major management regions within the study area. We addressed three sets of hypotheses associated with aspects of methodological, biological, and socio-political importance by asking (1) what is the consistency among implications of predicted changes based on the results of both ecological and evolutionary analyses; (2) what are the ecological and evolutionary implications of climate change considering either total regional diversity or distinct communities associated with major biomes; and (3) are there differences in management implications across regions? Our results indicate increasing Arctic richness through time that highlights a potential state shift across the Arctic landscape. However, within distinct ecological communities, we found a predicted decline in the range and effective population size of tundra species into several discrete refugial areas. Consistency in results based on a combination of both ecological and evolutionary approaches demonstrates increased statistical confidence by applying cross-discipline comparative analyses to conservation of biodiversity, particularly considering variable management regimes that seek to balance sustainable ecosystems with other anthropogenic values. Refugial areas for cold-adapted taxa appear to be persistent across both warm and cold climate phases and although fragmented, constitute vital regions for persistence of Arctic mammals.

Ecosphere↗

USGS2024

A unified approach to long-term population monitoring of grizzly bears in the Greater Yellowstone Ecosystem

Long-term wildlife research and monitoring programs strive to maintain consistent data collections and analytical methods. Incorporating new techniques is important but can render data sets incongruent and limit their potential to discern trends in demographic parameters. Integrated population models (IPMs) can address these limitations by combining data sources that may span different periods into a unified statistical framework while providing a holistic view of population dynamics. We developed an IPM in a Bayesian framework for grizzly bears ( Ursus arctos ) in the Greater Yellowstone Ecosystem. We coupled demographic data with multiple, independent population count data to link annual changes in abundance with vital rates over 4 decades (1983–2023). Abundance increased threefold from an estimated 270 individuals in 1984 to 1030 individuals in 2023. Parameter estimates indicated survival of bears ≥2 years of age was high, contributing to robust population growth during the 1980s (λ = 1.023 [50 % interquartile range = 0.993–1.082]) and 1990s (λ = 1.064 [1.023–1.103]). A slowing of population growth started around 2000 (2000s: λ = 1.030 [0.989–1.068]) and continued into the 2010s (λ = 1.021 [0.985–1.057]), due primarily to reductions in survival of bears <2 years of age. These findings corroborate previous research that identified density-dependent effects as a likely cause. The IPM framework provided greater certainty and understanding regarding the dynamic demographic characteristics of the population and serves as a powerful monitoring tool for this long-lived species. Implementation of the IPM allows timely dissemination of demographic data to help inform adaptive management strategies and policy decisions necessary for the continued management and conservation of this population. This robust and flexible monitoring system allows scientists to investigate the effects of a changing ecosystem on population dynamics, incorporate new data sources and statistical models, and respond to changes in monitoring needs for the population. We highlight the efficacy of the IPM in estimating and tracking demographic parameters for a long-lived species, while accommodating shifts in monitoring techniques and data collections typical of long-term wildlife conservation programs worldwide.

Idaho, Montana, Wyoming↗

USGS2003

Windows of opportunity: white-tailed deer and the dynamics of northern hardwood forests of the northeastern US

Herbivory, lighting regimes, and site conditions are among the most important determinants of forest regeneration success, but these are affected by a host of other factors such as weather, predation, human exploitation, pathogens, wind and fire. We draw together > 50 years of research on the Huntington Wildlife Forest in the central Adirondack Mountains of New York to explore regeneration of northern hardwoods. A series of studies each of which focused on a single factor failed to identify the cause of regeneration failure. However, integration of these studies led to broader understanding of the process of forest stand development and identified at least three interacting factors: lighting regime, competing vegetation and selective browsing by white-tailed deer (Odocoileus virginianus). The diverse 100-200 year-old hardwood stands present today probably reflect regeneration during periods of low deer density (< 2.0 deer/km super(2)) and significant forest disturbance. If this hypothesis is correct, forest managers can mimic these 'natural windows of opportunity' through manipulation of a few sensitive variables in the system. Further, these manipulations can be conducted on a relatively small geographic scale. Control of deer densities on a scale of 500 ha and understory American beech (Fagus grandifolia) on a scale of < 100 ha in conjunction with an even-aged regeneration system consistently resulted in successful establishment of desirable hardwood regeneration.

Journal for Nature Conservation↗

USGS2018

Ethanol and sodium acetate as a preservation method to delay degradation of environmental DNA

Environmental DNA (eDNA) samples that are collected from remote locations depend on rapid stabilization of the DNA. The degradation of eDNA in water samples is minimized when samples are stored at ≤ 4 °C. Developing a preservation technique to maintain eDNA integrity at room temperature would allow a wider range of locations to be sampled. We evaluated an ethanol and sodium acetate solution to maintain the integrity of the DNA samples for the time between collection and lab testing. For this evaluation, replicate water samples taken from a tank housing Asian carp were placed on ice or held at room temperature. At both temperatures, water samples were left untreated or were preserved with an ethanol and sodium acetate solution (EtOH–NaAc). Every day for 6 days following collection, a subset of the samples was removed from each preservation method and DNA was extracted and nuclear and mitochondrial markers were assayed with qPCR. Results showed comparable persistence of DNA between iced samples without the EtOH–NaAc treatment and samples that received EtOH–NaAc treatment that were kept at room temperature. We found that DNA can be amplified from preserved samples using an EtOH–NaAc solution after up to 7 days at room temperature.

Conservation Genetics Resources↗

USGS2010

Biosecurity Plan for Palmyra Atoll

This Biosecurity Plan for Palmyra Atoll was developed for The Nature Conservancy (TNC) Palmyra Program to refine and expand goals and objectives developed through the Conservation Action Plan process. The Biosecurity Plan is one in a series of adaptive management plans designed to achieve TNC's mission toward the protection and enhancement of native wildlife and habitat. The Biosecurity Plan focuses on ecosystem security, and specifically identifies and addresses issues related to non-native and potentially invasive species. The Plan attempts to identify pathways of invasion and strategies for preventing or reducing new introductions. Overall, the Biosecurity Plan provides a framework to implement and track the progress of conservation and restoration goals related to non-native species on Palmyra Atoll. Palmyra Atoll is one of the Northern Line Islands in the Pacific Ocean southwest of the Hawai`ian Islands. It consists of many heavily vegetated islets arranged in a horseshoe pattern around four lagoons and surrounded by a coral reef. At present, Palmyra Atoll harbors various non-native or invasive species in the terrestrial and marine ecosystems. The most notable examples of terrestrial invasive species include coconut trees (Cocos nucifera) and black rats (Rattus rattus). Although it is unclear whether they are non-native, coconut trees are currently the most dominant plant across Palmyra Atoll. They compete with native plant species for space and resources, and are potentially detrimental to seabirds dependent on native vegetation. Black rats are known to predate ground-nesting seabirds and are likely responsible for the lack of burrowing seabird reproduction on Palmyra Atoll. The most notable example of a marine invasive species is the corallimorph (Rhodactis howsei). Although Rhodactis howsei is a native species, it can take advantage of human-altered habitat and significantly change the natural habitat by aggressively outcompeting native corals. Although the extent and impacts of these and other non-native and (or) invasive species are not fully understood, they are clearly a threat to the native species and overall ecosystem integrity of Palmyra Atoll. In fact, non-native invasive species have been considered the most important threat to ecosystems in Hawai`i and the second most important threat to biodiversity world-wide. Palmyra Atoll is somewhat protected because of its remote location, but there are still potential pathways for the introduction of non-native and possibly invasive species. With the continued influx of aircraft and ocean vessels and their contents to and around Palmyra Atoll, we anticipate many more concerns related to the import and spread of non-native invasive species in the future. In terms of ecosystem security, prevention is the most effective and efficient tool for managing invasive species. There are various potential pathways for introduction and spread of non-native species within Palmyra Atoll's terrestrial and marine ecosystems. Identification of these pathways provides a first step in preventing introductions. We also recommend establishing, enhancing, and enforcing quarantine protocols to prevent future non-native species invasions. Other critical steps to minimize the impacts and spread of invasive species include early detection through inventory and monitoring, as well as containment, control, and management of non-native species already established at Palmyra Atoll. These efforts in combination with research and education will serve to inform management decisions related to ecosystem integrity. Along with reinstating ecosystem security, this Biosecurity Plan aims to evaluate new risk factors related to non-native and potentially invasive species. To that end, an adaptive management process of audit and review is highly recommended to ensure the implementation and efficacy of the management practices outlined above. In addition, it will be important to identify high r

Open-File Report↗

USGS2018

California State Waters Map Series — Offshore of Point Conception, California

Introduction In 2007, the California Ocean Protection Council initiated the California Seafloor Mapping Program (CSMP), designed to create a comprehensive seafloor map of high-resolution bathymetry, marine benthic habitats, and geology within the 3-nautical-mile limit of California’s State Waters. The CSMP approach is to create highly detailed seafloor maps through collection, integration, interpretation, and visualization of swath sonar data, acoustic backscatter, seafloor video, seafloor photography, high-resolution seismic-reflection profiles, and bottom-sediment sampling data. The map products display seafloor morphology and character, identify potential marine benthic habitats, and illustrate both the surficial seafloor geology and shallow subsurface geology. The Offshore of Point Conception map area is in the westernmost part of the Western Transverse Ranges geologic province, which is north of the California Continental Borderland. Significant clockwise rotation—at least 90°—since the early Miocene has been proposed for the Western Transverse Ranges province, and this region is presently undergoing north-south shortening. The offshore part of the map area lies south of the stee p south and west flanks of t he Santa Ynez Mountains . The crest of the range , which has a maximum elevation of about 340 m in the map area, lies about 5 km north and east of the arcuate shoreline. The onland part of the coastal zone is remote and sparsely populated. The road to Jalama Beach County Park provides the only public coastal access in the entire map area. North of this county park, the coastal zone is part of Vandenberg Air Force Base. South of Jalama Beach County Park, most of the coastal zone is part of the Cojo-Jalama Ranch, purchased by the Nature Conservancy in December 2017. A relatively small part of the coastal zone in the eastern part of the map area lies within the privately owned Hollister Ranch. The nearest significant commercial centers are Lompoc (population, about 42,000), about 10 km north of the map area, and Goleta (population, about 30,000), about 50 km east of the map area. The Union Pacific railroad tracks run west and northwest along the coast through the entire map area, within a few hundred meters of the shoreline. The map area has a long history of petroleum exploration, and the seafloor notably includes large asphalt mounds and pockmarks that result from petroleum seepage. Several offshore gas and oil fields were discovered, and some were developed, in and on the margin of California’s State Waters. Much of the shoreline in the Offshore of Point Conception map area is characterized by narrow beaches that have thin sediment cover above bedrock platforms, backed by low (10- to 20-m-high) cliffs that are capped by a coastal terrace. Beaches are subject to wave erosion during winter storms, followed by gradual sediment recovery or accretion in the late spring, summer, and fall months during the gentler wave climate. The map area lies in the west-central part of the Santa Barbara littoral cell, which is characterized by west-to-east transport of sediment from Point Arguello on the northwest to Hueneme and Mugu Canyons on the southeast. Sediment supply to the map area is mainly from relatively small coastal watersheds, including the Jalama Creek–Espada Creek drainage basin (about 63 km 2 ), as well as Cañada del Jolloru, Black Canyon, Wood Canyon, Cañada del Cojo, and Barranca Honda. Coastal-watershed discharge and sediment load are highly variable, characterized by brief large events during major winter storms and long periods of low (or no) flow and minimal sediment load between storms. In recent (recorded) history, the majority of high-discharge, high-sediment-flux events have been associated with El Niño phases of the El Niño–Southern Oscillation climatic pattern. Following the coastline, the shelf bends to the north and northwest around Point Conception, and the trend of the shelf break changes from about 298° to 241° azimuth. Shelf width ranges from about 5 km south of Point Conception to about 11 km northwest of it; the slope ranges from about 1.0° to 1.2° to about 0.7° south and northwest of Point Conception, respectively. Southwest of Point Conception, the shelf break and upper slope are incised by a 600-m-wide, 20- to 30-m-deep, south-facing trough, one of five heads of the informally named Arguello submarine canyon. The map area is located at a major biogeographic transition zone between the east-west-trending Santa Barbara Channel region of the Southern California Bight and the northwest-trending central California coast. North of Point Conception, the coast is subjected to high wave exposure from the north, west, and south, as well as consistently strong upwelling that brings cold, nutrient-rich waters to the surface. Southeast of Point Conception, the Santa Barbara Channel is largely protected from strong north swells by Point Conception and from south swells by the Channel Islands; surface waters are warmer, and upwelling is weak and seasonal. Seafloor habitats in the broad Santa Barbara Channel region consist of significant amounts of soft, unconsolidated sediment interspersed with isolated areas of rocky habitat that support kelp-forest communities in the nearshore and rocky-reef communities in deeper water. The potential marine benthic habitat types mapped in the Offshore of Point Conception map area are directly related to its Quaternary geologic history, geomorphology, and active sedimentary processes. These potential habitats lie primarily within the Shelf (continental shelf) but also partly within the Flank (basin flank or continental slope) megahabitats. The fairly homogeneous seafloor of sediment and low-relief bedrock provides characteristic habitat for rockfish, groundfish, crabs, shrimp, and other marine benthic organisms. Several areas of smooth sediment form nearshore terraces that have relatively steep, smooth fronts, which are attractive to groundfish. Below the steep shelf break, soft, unconsolidated sediment is interrupted by the heads of several submarine canyons, gullies, and rills, also good potential habitat for rockfish. The map area includes the large (58.3 km 2 ) Point Conception State Marine Reserve.

California↗

USGS2013

Vegetation projections for Wind Cave National Park with three future climate scenarios: Final report in completion of Task Agreement J8W07100052

Introduction The effects of climate change on the natural resources protected by Parks will likely be substantial, but geographically variable, due to local variation in climate trajectories and differences among ecosystems in their vulnerability to climate change. The projections of general circulation models (GCMs) indicate the possible magnitude and direction of future climate change for a region, but the utility of these projections for more local scales, those of individual National Park Service (NPS) units, are more uncertain because the coarse-scale GCMs lack much of the topographic detail that alters local climates. In addition, complex, interacting effects of temperature, precipitation, atmospheric CO 2 concentrations, fire, and herbivores on the vegetation that is the foundational natural resource of many NPS units present challenges in assessing the effects of projected future climates on plant and animal assemblages managed by the NPS. In spring 2009, Wind Cave National Park (WICA) served as a case study in a workshop assessing the use of scenario planning as a tool for park management planning in the face of rapidly changing climate. One outcome of the workshop was the recognized need for quantitative models to better understand the range of possible vegetation changes under different future climates and management decisions. This report addresses this need; it describes our adaptation of a dynamic global vegetation model (DGVM) to WICA vegetation and the resulting projections of future vegetation under three future climate scenarios and 11 management scenarios determined by Park natural resource managers. Wind Cave National Park lies along a narrow transition zone between the ponderosa pine (Pinus ponderosa) forests of the Black Hills and the mixed grass prairie that once extended with few interruptions over the lower, gentler terrain, subject to warmer, drier climate to the east and south of the Park. The location and character of this transition is strongly influenced by fire frequency and intensity (Brown and Sieg 1999). Furthermore, the mixed grass prairie occupies a broader transition zone between eastern tallgrass prairie and the shortgrass prairie of the western Great Plains. The dominance of species characteristic of these two prairie types varies with soil moisture availability, evaporative demand, and recent grazing history (Cogan et al. 1999). In addition, Wind Cave lies near the midpoint of a long gradient of C 3 (cool season) grass dominance to the north and C 4 (warm season) grass dominance to the south. The ecotonal position of WICA may make it particularly sensitive to climate change. For example, small changes in fire frequency and/or intensity and the vigor of trees vs. grass could dramatically shift the proportions of these two lifeforms. The Park hydrology is also sensitive to changes in the balance between infiltration of precipitation and evapotranspiration, as on average, only a small fraction of annual precipitation reaches the deeper soil layers that feed permanent streamflow. The resources at risk at Wind Cave NP include the Cave itself, as well as small backcountry caves, a genetically important bison herd, and other prairie species including the black-tailed prairie dog and endangered black-footed ferrets. All of these resources will be directly affected by climate change impacts on vegetation and hydrology. Natural resource management challenges at WICA are substantial, diverse, and intertwined. Aboveground, the park has been recognized as exemplary for its high quality vegetation (Marriot et al. 1999), though the park is relatively small for the diversity of vegetation types and species that it supports. Even without a changing climate, maintaining the integrity of the plant communities is complicated by the park’s legislated responsibility to maintain viable populations of bison, elk and pronghorn. In addition, the federally endangered black-footed ferret was recently re-introduced to the park. This species requires large extents of prairie dog towns for prey and habitat. Prairie dogs impact vegetation by constant clipping, grazing and soil disturbance, thereby affecting plant composition and productivity. Moreover, naturally high interannual climate variability and the strong influence of precipitation on grass productivity in this region combine to yield high interannual variability in the amount of forage available for the wildlife that the park is tasked to maintain. Finally, fire, which is now primarily controlled by WICA and NPS Northern Great Plains fire management programs, is intertwined with all other natural resource issues at WICA, as it can impact prairie dog colony and forest expansion, ungulate foraging behavior, invasive plant species, and hydrological processes. Although not capable of capturing all of these complexities, dynamic vegetation models do provide a means for quantitatively projecting vegetation futures in future climates under plausible fire and grazing regimes. Our work uses the DGVM MC1 to simulate the effects of future climate projections and management practices on the vegetation of WICA. MC1 is designed to project potential vegetation as influenced by natural processes and hence is appropriate for national parks, where conservation of native biota and ecosystems is of great importance. Since the initial application of MC1 to a small portion of WICA (Bachelet et al. 2000), the model has been altered to improve model performance with the inclusion of dynamic fire. Applying this improved version to WICA required substantial recalibration, during which we have made a number of improvements to MC1 that will be incorporated as permanent changes. In this report we document these changes and our calibration procedure following a brief overview of the model. We compare the projections of current vegetation to the current state of the park and present projections of vegetation dynamics under future climates downscaled from three GCMs selected to represent the existing range in available GCM projections. In doing so, we examine the consequences of different management options regarding fire and grazing, major aspects of biotic management at Wind Cave.

South Dakota↗

USGS2025

Pit tag application in native freshwater mussels: Case studies across small, medium, and large rivers

Since their first use in the mid-1980s, external passive integrated transponder (PIT) tags have facilitated innovative investigations into multiple biological traits of animals. For native freshwater mussels, PIT tags are frequently used in capture-mark-recapture applications because they allow repeated, noninvasive sampling, are easy to apply, have high retention rates, and have negligible short-term effects on growth and survival. Because of these traits, resource managers and scientists are using PIT-tagged animals to estimate survival and movement of mussels associated with restoration efforts. However, consistency is limited in how PIT tags are affixed, monitored, and reported. Thus, our objectives were to (1) share our collective experiences in PIT tagging mussels across three case studies in small, medium, and large rivers and (2) propose guidelines for tagging and reporting data from PIT tag studies with native freshwater mussels to facilitate comparisons across future studies. The number of studies that have marked mussels with PIT tags has increased over the past 10 years. The ability to detect mussels using PIT tags has substantially advanced research in three areas of mussel ecology: (1) estimating vital rates (e.g., growth and survival), (2) tracking movements and behaviors of captively propagated, wild, and translocated individuals, and (3) improving our understanding of life history traits, such as reproductive timing. Each case study offers insights on tagging methods, tag loss, tag retention, and monitoring frequency across multiple species that range in conservation status from common to rare. We conclude with best-practice guidelines for placing PIT tags on freshwater mussels and a list of variables that could be reported in future studies to facilitate cross-system comparisons.

Freshwater Mollusk Biology and Conservation↗

USGS2024

Ecological trade-offs associated with fuel breaks in the sagebrush ecosystem

Background Unprecedented wildfire frequency, fueled by invasive annual grasses, threatens sagebrush ecosystems. To suppress wildfire and conserve sagebrush, land management agencies have installed fuel breaks across the sagebrush biome. However, despite the potential reduction in wildfire, fuel breaks may have ecological costs. Determining an acceptable balance between risks and benefits of fuel breaks is needed to avoid accelerating sagebrush loss, annual grass invasion, and habitat degradation. To evaluate the potential for ecological trade-offs to occur, we characterized the contexts in which known fuel breaks currently exist. We synthesized spatial data on all known fuel breaks and a suite of variables that may contribute to fuel break risks and benefits, including burn probabilities, predicted fuel break effectiveness, linear infrastructure, invasive annual grass cover, soil moisture conditions that confer resistance to invasion and resilience to disturbance, and priority wildlife habitats across the sagebrush biome. Results We found that within the sagebrush biome, fuel breaks are generally located in areas with high burn probability and are thus positioned well to intercept potential wildfires. However, fuel breaks are also frequently positioned in areas with lower predicted fuel break effectiveness relative to the sagebrush biome overall. Fuel breaks also are spatially associated with high invasive grass cover, indicating the need to better understand the causal relationship between fuel breaks and annual invasive grasses. We also show that the fuel break network is dense within priority wildlife habitats. Dense fuel breaks within wildlife habitats may trade off wildfire protection for decreased integrity of such habitats. Conclusions Our analyses describe the potential for fuel breaks to invoke ecological trade-offs and show that the balance of risks and benefits differs across sagebrush ecosystems. Strategic research and actions are needed to evaluate which factors tip the balance towards maximizing wildfire suppression while minimizing risk to sensitive ecological resources.

Arizona, California, Colorado, Idaho, Montana, Nev↗

USGS2025

How accurately does eDNA reflect the spatial distribution of cold-water fish? Field validation from a temperate lake

Applications of environmental DNA (eDNA) based detection technology to evaluate the distribution of aquatic organisms are increasing; yet field validations of eDNA are important to measure accuracy in study systems. To successfully apply this technology to species conservation, it is critical to understand how both species biology and environmental conditions affect the accuracy of inference from eDNA detection data. We implemented a field assessment of the accuracy and spatial resolution of eDNA-based species distributions for a native cold-water, schooling fish, cisco Coregonus artedi , that has been reintroduced to a deep temperate lake. We leveraged a combination of acoustic telemetry, providing known spatial locations of tagged fish, and lake-wide eDNA sampling to infer their distribution in Keuka Lake, New York, USA. Sub-surface (12 m and 18 m depths) eDNA samples were collected to accommodate the diel vertical migration behaviour of this fish species. The results of this study validated the accuracy of positive eDNA detections with the distribution of tagged fish to coarse spatial scales. Yet, several fine-scale locations revealed a mismatch between eDNA and acoustic telemetry detections; consistent with rapid transport of genetic material via lake currents. Empirical measurements of lake currents using drifters found cisco eDNA detections could deviate from specimens' source locations by as much as 3.3 km at 12 m depth or 1.5 km at 18 m depth over a 24 h transport period. Our study indicates that accurate species distributions estimated from eDNA sampling in lakes may require further understanding of transport mechanisms and persistence of environmental genetic material to relate point detections to source animal locations. Integrating eDNA sampling with additional data collection of species biology and environmental conditions will increase the spatial resolution of fish distribution assessments.

New York↗

USGS2019

Monitoring boreal avian populations: How can we estimate trends and trajectories from noisy data?

Substantial effort has been dedicated to developing reliable monitoring schemes for North American bird populations, but our ability to monitor bird populations in the boreal forest remains limited because of the sparsity of long-term data sets, particularly in northerly regions. Given the importance of the boreal forest for many migratory birds, we set out to (1) summarize the main challenges associated with monitoring avian populations, (2) describe the available statistical tools for population monitoring and their applications, and (3) identify future directions to overcome current challenges in monitoring bird populations in the boreal forest. Defining and delineating populations of interest and identifying the drivers that affect those populations present the greatest current challenges. This is because migratory birds may be affected by many population-limiting processes at different stages of their annual life cycles. These factors are often hierarchically structured and can influence populations at the local, regional, or continental scales. Some of the challenges associated with delineating populations and identifying population drivers can be addressed via the plethora of sampling and analytic methods available to examine population change over time. Choosing the proper analytic methods depends on the goals of the study and the nature of the data such as single or multiple populations, repeated occurrence or count-based surveys, or demographic rates. Recent advances in hierarchical and integrated population models make these analytic approaches some of the most promising avenues for the development of future methods. However, these tools require large data sets, and acquiring sufficient data on bird populations and potential explanatory variables is difficult in the boreal forest. If the current challenges to monitoring birds in the boreal forest are to be overcome, serious effort should be dedicated to integrating existing data and making them accessible. Enhancing survey effort through multispecies surveys will also play an important role. Implementing spatially balanced sampling plans with a rotating panel design could balance the trade-offs between spatial versus temporal replication at an affordable cost. Improving the accessibility of environmental covariates that are spatially and temporally explicit would also enable development of mechanistic population models that improve our understanding of migratory bird population dynamics. Finally, given that long-term monitoring programs can take many decades before delivering reliable population trends and that organizational priorities often change over time, we suggest that collaborative efforts will help ensure the long-term survival of new monitoring programs.

Avian Conservation and Ecology↗

USGS2013

Tracking animals in freshwater with electronic tags: past, present and future

Considerable technical developments over the past half century have enabled widespread application of electronic tags to the study of animals in the wild, including in freshwater environments. We review the constraints associated with freshwater telemetry and biologging and the technical developments relevant to their use. Technical constraints for tracking animals are often influenced by the characteristics of the animals being studied and the environment they inhabit. Collectively, they influence which and how technologies can be used and their relative effectiveness. Although radio telemetry has historically been the most commonly used technology in freshwater, passive integrated transponder (PIT) technology, acoustic telemetry and biologgers are becoming more popular. Most telemetry studies have focused on fish, although an increasing number have focused on other taxa, such as turtles, crustaceans and molluscs. Key technical developments for freshwater systems include: miniaturization of tags for tracking small-size life stages and species, fixed stations and coded tags for tracking large samples of animals over long distances and large temporal scales, inexpensive PIT systems that enable mass tagging to yield population- and community-level relevant sample sizes, incorporation of sensors into electronic tags, validation of tag attachment procedures with a focus on maintaining animal welfare, incorporation of different techniques (for example, genetics, stable isotopes) and peripheral technologies (for example, geographic information systems, hydroacoustics), development of novel analytical techniques, and extensive international collaboration. Innovations are still needed in tag miniaturization, data analysis and visualization, and in tracking animals over larger spatial scales (for example, pelagic areas of lakes) and in challenging environments (for example, large dynamic floodplain systems, under ice). There seems to be a particular need for adapting various global positioning system and satellite tagging approaches to freshwater. Electronic tagging provides a mechanism to collect detailed information from imperilled animals and species that have no direct economic value. Current and future advances will continue to improve our knowledge of the natural history of aquatic animals and ecological processes in freshwater ecosystems while facilitating evidence-based resource management and conservation.

Animal Biotelemetry↗

USGS2018

Landscape connectivity for bobcat (Lynx rufus) and lynx (Lynx canadensis) in the Northeastern United States

Landscape connectivity is integral to the persistence of metapopulations of wide ranging carnivores and other terrestrial species. The objectives of this research were to investigate the landscape characteristics essential to use of areas by lynx and bobcats in northern New England, map a habitat availability model for each species, and explore connectivity across areas of the region likely to experience future development pressure. A Mahalanobis distance analysis was conducted on location data collected between 2005 and 2010 from 16 bobcats in western Vermont and 31 lynx in northern Maine to determine which variables were most consistent across all locations for each species using three scales based on average 1) local (15 minute) movement, 2) linear distance between daily locations, and 3) female home range size. The bobcat model providing the widest separation between used locations and random study area locations suggests that they cue into landscape features such as edge, availability of cover, and development density at different scales. The lynx model with the widest separation between random and used locations contained five variables including natural habitat, cover, and elevation—all at different scales. Shrub scrub habitat—where lynx’s preferred prey is most abundant—was represented at the daily distance moved scale. Cross validation indicated that outliers had little effect on models for either species. A habitat suitability value was calculated for each 30 m 2 pixel across Vermont, New Hampshire, and Maine for each species and used to map connectivity between conserved lands within selected areas across the region. Projections of future landscape change illustrated potential impacts of anthropogenic development on areas lynx and bobcat may use, and indicated where connectivity for bobcats and lynx may be lost. These projections provided a guide for conservation of landscape permeability for lynx, bobcat, and species relying on similar habitats in the region.

PLoS ONE↗

USGS2022

Integrating principles and tools of decision science into value-driven watershed planning for compensatory mitigation

Several environmental policies strive to restore impaired ecosystems and could benefit from a consistent and transparent process — co-developed with key stakeholders — to prioritize impaired ecosystems for restoration activities. The Clean Water Act, for example, establishes reallocation mechanisms to transfer ecosystem services from sites of disturbance to compensation sites to offset aquatic resource functions that are unavoidably lost through land development. However, planning for the prioritization of compensatory mitigation areas is often hampered by decision-making processes that fall into a myopic decision frame because they are not co-produced with stakeholders. In this study, we partnered with domain experts from the North Carolina Division of Mitigation Services (NCDMS) to co-develop a real-world decision framework to prioritize catchments by potential for the development of mitigation projects following principles of a structured decision-making process and knowledge co-production. Following an iterative decision analysis cycle, domain experts revised foundational components of the decision framework and progressively added complexity and realism as they gained additional insights or more information became available. Through the course of facilitated in-person and remote interactions, the co-development of a decision framework produced three main ‘breakthroughs’ from the perspective of the stakeholder group: a) recognition of the problem as a multi-objective decision driven by several values in addition to biogeophysical goals (e.g., functional uplift; restoring or enhancing lost functionality of ecosystems), b) that the decision comprises a linked and sequential planning-to-implementation process, and c) future risk associated with land-use and climate change must be considered. We also present an interactive tool for ‘on-the-fly’ assessment of alternatives and tradeoff analysis, allowing domain experts to quickly test, react to, and revise prioritization strategies. The decision framework described in this study is not limited to the prioritization of compensatory mitigation activities across North Carolina, but rather serves as a framework to prioritize a wide range of restoration, conservation, and resource allocation activities in similar environmental contexts across the nation.

Ecological Applications↗

USGS2016

Consequences of changes in vegetation and snow cover for climate feedbacks in Alaska and northwest Canada

Changes in vegetation and snow cover may lead to feedbacks to climate through changes in surface albedo and energy fluxes between the land and atmosphere. In addition to these biogeophysical feedbacks, biogeochemical feedbacks associated with changes in carbon (C) storage in the vegetation and soils may also influence climate. Here, using a transient biogeographic model (ALFRESCO) and an ecosystem model (DOS-TEM), we quantified the biogeophysical feedbacks due to changes in vegetation and snow cover across continuous permafrost to non-permafrost ecosystems in Alaska and northwest Canada. We also computed the changes in carbon storage in this region to provide a general assessment of the direction of the biogeochemical feedback. We considered four ecoregions, or Landscape Conservations Cooperatives (LCCs; including the Arctic, North Pacific, Western Alaska, and Northwest Boreal). We examined the 90 year period from 2010 to 2099 using one future emission scenario (A1B), under outputs from two general circulation models (MPI-ECHAM5 and CCCMA-CGCM3.1). We found that changes in snow cover duration, including both the timing of snowmelt in the spring and snow return in the fall, provided the dominant positive biogeophysical feedback to climate across all LCCs, and was greater for the ECHAM (+3.1 W m −2 decade −1 regionally) compared to the CCCMA (+1.3 W m −2 decade −1 regionally) scenario due to an increase in loss of snow cover in the ECHAM scenario. The greatest overall negative feedback to climate from changes in vegetation cover was due to fire in spruce forests in the Northwest Boreal LCC and fire in shrub tundra in the Western LCC (−0.2 to −0.3 W m −2 decade −1 ). With the larger positive feedbacks associated with reductions in snow cover compared to the smaller negative feedbacks associated with shifts in vegetation, the feedback to climate warming was positive (total feedback of +2.7 W m −2 decade regionally in the ECHAM scenario compared to +0.76 W m −2 decade regionally in the CCCMA scenario). Overall, increases in C storage in the vegetation and soils across the study region would act as a negative feedback to climate. By exploring these feedbacks to climate, we can reach a more integrated understanding of the manner in which climate change may impact interactions between high-latitude ecosystems and the global climate system.

Environmental Research Letters↗

USGS2022

Divergent climate impacts on C3 versus C4 grasses imply widespread 21st century shifts in grassland functional composition

Aim Grasslands cover a third of Earth's landmass and provide critical ecosystem services. Anticipating how perennial C 3 (cool-season) and C 4 (warm-season) grasses respond to climate change will be key to predicting future composition and functioning of grasslands. Here, we evaluate environmental drivers of C 3 and C 4 perennial distributions and assess how C 3 and C 4 grass distributions shift in response to future climate change. Location Western United States. Methods We developed integrated species distribution models to identify climate and soil drivers of relative abundance of C 3 and C 4 perennial grasses. We then created projections of species abundances under future climate and evaluated when and where projected shifts in relative abundance were robust across climate models. Results Historically, C 3 grasses occupied areas with lower temperature and more variable precipitation regimes, while C 4 grasses occupied areas of higher temperature, greater temperature variability and greater warm-season precipitation. C 4 species also occupied narrower soil texture niches. In response to future climate change, C 3 grass abundance declined across 74% of areas, while C 4 abundance increased across 66% of areas. C 3 grasses expanded in mid- to higher-latitude areas with increasing temperature and decreasing seasonality of precipitation. In contrast, C 4 grasses increased in higher-latitude regions, but declined in lower-latitude, dryer regions. Results were surprisingly robust across climate scenarios, suggesting high confidence in the direction of these future changes. Main Conclusions Findings imply C 3 and C 4 perennial grasses will have highly divergent responses to climate change that may result in grassland functional compositional changes. Increasing temperatures and precipitation variability may favour some C 4 grasses, but C 4 habitat expansion may be constrained by soil conditions in western USA. Results provide actionable insights for anticipating the impacts of climate change on grass-dominated and co-dominated ecosystems and improving large-scale conservation and restoration efforts.

Diversity and Distributions↗

USGS2015

How big of an effect do small dams have? Using geomorphological footprints to quantify spatial impact of low-head dams and identify patterns of across-dam variation

Longitudinal connectivity is a fundamental characteristic of rivers that can be disrupted by natural and anthropogenic processes. Dams are significant disruptions to streams. Over 2,000,000 low-head dams (<7.6 m high) fragment United States rivers. Despite potential adverse impacts of these ubiquitous disturbances, the spatial impacts of low-head dams on geomorphology and ecology are largely untested. Progress for research and conservation is impaired by not knowing the magnitude of low-head dam impacts. Based on the geomorphic literature, we refined a methodology that allowed us to quantify the spatial extent of low-head dam impacts (herein dam footprint), assessed variation in dam footprints across low-head dams within a river network, and identified select aspects of the context of this variation. Wetted width, depth, and substrate size distributions upstream and downstream of six low-head dams within the Upper Neosho River, Kansas, United States of America were measured. Total dam footprints averaged 7.9 km (3.0–15.3 km) or 287 wetted widths (136–437 wetted widths). Estimates included both upstream (mean: 6.7 km or 243 wetted widths) and downstream footprints (mean: 1.2 km or 44 wetted widths). Altogether the six low-head dams impacted 47.3 km (about 17%) of the mainstem in the river network. Despite differences in age, size, location, and primary function, the sizes of geomorphic footprints of individual low-head dams in the Upper Neosho river network were relatively similar. The number of upstream dams and distance to upstream dams, but not dam height, affected the spatial extent of dam footprints. In summary, ubiquitous low-head dams individually and cumulatively altered lotic ecosystems. Both characteristics of individual dams and the context of neighboring dams affected low-head dam impacts within the river network. For these reasons, low-head dams require a different, more integrative, approach for research and management than the individualistic approach that has been applied to larger dams.

PLoS ONE↗