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USGS2022

Balancing model generality and specificity in management-focused habitat selection models for Gunnison sage-grouse

Identifying, protecting, and restoring habitats for declining wildlife populations is foundational to conservation and recovery planning for any species at risk of decline. Resource selection analysis is a key tool to assess habitat and prescribe management actions. Yet, it can be challenging to map suitable resource conditions across a wide range of ecological contexts and use the resulting models to identify effective and universal habitat improvement actions. We developed a management-centric modeling approach that sought to balance the need to evaluate the consistency of key habitat conditions and improvement actions across multiple, distinct populations, while allowing context-specific environmental variables and spatial scales to nuance selection responses that form the basis of location-specific management prescriptions. To demonstrate this approach, we developed a set of habitat selection models for Gunnison sage-grouse ( Centrocercus minimus ), a threatened species under the U.S. Endangered Species Act. Conservation, species recovery, and habitat management efforts are needed in six isolated satellite populations (San Miguel, Crawford, Piñon Mesa, Dove Creek, Cerro Summit-Cimarron-Sims, and Poncha Pass) where environmental conditions differ, and the already small number of birds are declining. We used multi-scale and seasonal resource selection analyses to quantify relationships between environmental conditions and sites used by animals. All models included key habitat variables often altered through management actions to assess their differential influences across models. We found important similarities and differences among satellites, indicating that, although some rules of thumb are generally well-grounded, the consideration of population-specific environmental differences could increase the efficiency of local habitat improvement actions. Sage-grouse also had diverse responses to resource conditions at different scales, indicating that regional spatial (e.g., landscape) and local patch scale can differentially influence expected habitat improvements associated with where such management actions are implemented. Although context variables such as topography cannot be manipulated, sage-grouse associations revealed information that could guide the siting of improvement actions. This approach to balancing management objectives associated with habitat assessment may benefit spatially-structured populations with different environmental contexts and species with complex habitat needs and associations.

Colorado↗

USGS2011

Learning and adaptation in the management of waterfowl harvests

A formal framework for the adaptive management of waterfowl harvests was adopted by the U.S. Fish and Wildlife Service in 1995. The process admits competing models of waterfowl population dynamics and harvest impacts, and relies on model averaging to compute optimal strategies for regulating harvest. Model weights, reflecting the relative ability of the alternative models to predict changes in population size, are used in the model averaging and are updated each year based on a comparison of model predictions and observations of population size. Since its inception the adaptive harvest program has focused principally on mallards ( Anas platyrhynchos ), which constitute a large portion of the U.S. waterfowl harvest. Four competing models, derived from a combination of two survival and two reproductive hypotheses, were originally assigned equal weights. In the last year of available information (2007), model weights favored the weakly density-dependent reproductive hypothesis over the strongly density-dependent one, and the additive mortality hypothesis over the compensatory one. The change in model weights led to a more conservative harvesting policy than what was in effect in the early years of the program. Adaptive harvest management has been successful in many ways, but nonetheless has exposed the difficulties in defining management objectives, in predicting and regulating harvests, and in coping with the tradeoffs inherent in managing multiple waterfowl stocks exposed to a common harvest. The key challenge now facing managers is whether adaptive harvest management as an institution can be sufficiently adaptive, and whether the knowledge and experience gained from the process can be reflected in higher-level policy decisions.

Journal of Environmental Management↗

USGS2013

Empirical estimates to reduce modeling uncertainties of soil organic carbon in permafrost regions: a review of recent progress and remaining challenges

The vast amount of organic carbon (OC) stored in soils of the northern circumpolar permafrost region is a potentially vulnerable component of the global carbon cycle. However, estimates of the quantity, decomposability, and combustibility of OC contained in permafrost-region soils remain highly uncertain, thereby limiting our ability to predict the release of greenhouse gases due to permafrost thawing. Substantial differences exist between empirical and modeling estimates of the quantity and distribution of permafrost-region soil OC, which contribute to large uncertainties in predictions of carbon–climate feedbacks under future warming. Here, we identify research challenges that constrain current assessments of the distribution and potential decomposability of soil OC stocks in the northern permafrost region and suggest priorities for future empirical and modeling studies to address these challenges.

Environmental Research Letters↗

USGS2013

Selenium in irrigated agricultural areas of the western United States

Selenium was recognized as an important aquatic contaminant following the identification of widespread deformities in waterfowl at the agricultural drainage evaporation ponds of the Kesterson Reservoir (California) in 1983. Since then, California has been the focal point for global research and management of Se contamination. We analyzed the history and current developments in science, policy, and management of irrigation-induced Se contamination in California. In terms of management, we evaluated the effects of improvements in the design of local attenuation methods (drainage reuse and evaporation ponds) in conjunction with the development of programs for Se load reductions at the regional scale (namely the Grassland Bypass Project). In terms of policy, the USEPA is currently working on site-specific water quality criteria for the San Francisco Bay Delta that may be a landmark for future legislation on Se in natural water bodies. We provide a critical analysis of this approach and discuss challenges and opportunities in expanding it to other locations such as the Salton Sea. Management lessons learned in California and the novel policy approach may help prevent future events of Se contamination.

Journal of Environmental Quality↗

USGS2020

Mitochondrial genome diversity and population mitogenomics of Polar cod (Boreogadus saida) and Arctic dwelling gadoids

High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on the mitochondrial genome. We found little population-level structure within all four species with the clear exception of Gulf of Alaska saffron cod ( Eleginus gracilis ). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within polar cod ( Boreogadus saida ) and saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in complex I (ND genes) in polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

Alaska↗

USGS2025

Leveraging invasive mussel contaminant survey data for stepwise prioritization of chemicals of potential concern in the Great Lakes basin

Historical and ongoing anthropogenic activities coupled with advancements in analytical techniques have led to the detection of large numbers of contaminants in the Laurentian Great Lakes. Consequently, identifying and prioritizing chemicals likely to cause ecological harm represents a challenge for natural resource managers. Previous prioritization efforts have focused on contaminants in sediment, water, and passive samplers, which may not be representative of compounds that bioaccumulate in aquatic organisms. Consequently, this study adopted a stepwise method to prioritize chemicals of potential concern detected in dreissenid mussels from samples collected across the Great Lakes from 2009–2018. The stepwise method considered environmental fate, detection frequency, and exceedance of toxicity quotients based on ecotoxicological effect concentrations. Overall, 153 compounds out of 267 analyzed were detected in dreissenid mussels, 47 of which had water quality effect concentrations, 56 had apical effect concentrations (Tier 1 ECOTOX or apical screening), 17 had nonapical effect concentrations (Tier 2 ECOTOX, Cytotoxic Burst, and ToxCast) and 33 had estimated effect concentrations (quantitative structure-activity relationship, estimated screening, and pharmacological potency). Of the compounds with water quality effect concentrations, nine were designated as high priority, including the herbicide atrazine and five polycyclic aromatic hydrocarbons that were previously identified as potentially hazardous within other matrices. Similar contaminants were identified as high priority in a related study of native unionid mussels in the Great Lakes. A total of 27 compounds were low priority, suggesting that these contaminants do not warrant further action based on this dataset. Overall, these findings will facilitate the development of management strategies to mitigate the effects of contaminants on aquatic organisms within the Great Lakes.

Great Lakes basin↗

USGS2007

Acid rain in Shenandoah National Park, Virginia

Visitors to Shenandoah National Park (SNP) enjoy the animal and plant life and the scenery but may not realize how vulnerable these features are to various threats, such as invasion of exotic plants and insects, improper use of park resources by humans, and air and water pollution. The National Park Service strives to protect natural resources from such threats to ensure that the resources will be available for enjoyment now and in the future. Because SNP has limited influence over the air pollution that envelops the region, acidic deposition--commonly known as acid rain--is one of the more challenging threats facing park managers. With the help of U.S. Geological Survey (USGS) scientists, park managers can understand how acid rain interacts with ground- and surface-water resources, which enables them to explain why reductions in air pollution can help preserve park resources. Such understanding also provides essential insight into ecosystem processes, as managers strive to unravel and resolve other environmental problems that are interrelated to acid rain.

Virginia↗

USGS2021

Temporal influences on selenium partitioning, trophic transfer, and exposure in a major U.S. river

Hydrologic and irrigation regimes mediate the timing of selenium (Se) mobilization to rivers, but the extent to which patterns in Se uptake and trophic transfer through recipient food webs reflect the temporal variation in Se delivery is unknown. We investigated Se mobilization, partitioning, and trophic transfer along approximately 60 river miles of the selenium-impaired segment of the Lower Gunnison River (Colorado, USA) during six sampling trips between June 2015 and October 2016. We found temporal patterns in Se partitioning and trophic transfer to be independent of those in dissolved Se concentrations and that the recipient food web sustained elevated Se concentrations from earlier periods of high Se mobilization. Using an ecosystem-scale Se accumulation model tailored to the Lower Gunnison River, we predicted that the endangered Razorback Sucker ( Xyrauchen texanus ) and Colorado Pikeminnow ( Ptychocheilus lucius ) achieve whole-body Se concentrations exceeding aquatic life protection criteria during periods of high runoff and irrigation activity (April–August) that coincide with susceptible phases of reproduction and early-life development. The results of this study challenge assumptions about Se trophodynamics in fast-flowing waters and introduce important considerations for the management of Se risks for biota in river ecosystems.

Colorado↗

USGS2012

Mapping river bathymetry with a small footprint green LiDAR: Applications and challenges

Airborne bathymetric Light Detection And Ranging (LiDAR) systems designed for coastal and marine surveys are increasingly sought after for high-resolution mapping of fluvial systems. To evaluate the potential utility of bathymetric LiDAR for applications of this kind, we compared detailed surveys collected using wading and sonar techniques with measurements from the United States Geological Survey’s hybrid topographic⁄ bathymetric Experimental Advanced Airborne Research LiDAR (EAARL). These comparisons, based upon data collected from the Trinity and Klamath Rivers, California, and the Colorado River, Colorado, demonstrated that environmental conditions and postprocessing algorithms can influence the accuracy and utility of these surveys and must be given consideration. These factors can lead to mapping errors that can have a direct bearing on derivative analyses such as hydraulic modeling and habitat assessment. We discuss the water and substrate characteristics of the sites, compare the conventional and remotely sensed river-bed topographies, and investigate the laser waveforms reflected from submerged targets to provide an evaluation as to the suitability and accuracy of the EAARL system and associated processing algorithms for riverine mapping applications.

Journal of the American Water Resources Associatio↗

USGS2020

Subspecies differentiation in an enigmatic chaparral shrub species

Premise Delimiting biodiversity units is difficult in organisms in which differentiation is obscured by hybridization, plasticity, and other factors that blur phenotypic boundaries. Such work is more complicated when the focal units are subspecies, the definition of which has not been broadly explored in the era of modern genetic methods. Eastwood manzanita ( Arctostaphylos glandulosa Eastw.) is a widely distributed and morphologically complex chaparral shrub species with much subspecific variation, which has proven challenging to categorize. Currently 10 subspecies are recognized, however, many of them are not geographically segregated, and morphological intermediates are common. Subspecies delimitation is of particular importance in this species because two of the subspecies are rare. The goal of this study was to apply an evolutionary definition of “subspecies” to characterize structure within Eastwood manzanita. Methods We used publicly available geospatial environmental data and reduced‐representation genome sequencing to characterize environmental and genetic differentiation among subspecies. In addition, we tested whether subspecies could be differentiated by environmentally associated genetic variation. Results Our analyses do not show genetic differentiation among subspecies of Eastwood manzanita, with the exception of one of the two rare subspecies. In addition, our environmental analyses did not show ecological differentiation, though limitations of the analysis prevent strong conclusions. Conclusions Genetic structure within Eastwood manzanita does not correspond to current subspecies circumscriptions, but rather reflects geographic distribution. Our study suggests that subspecies concepts need to be reconsidered in long‐lived plant species, especially in the age of next‐generation sequencing.

American Journal of Botany↗

USGS2019

Reproductive failure in the Eastern Migratory Population: The interaction of research and management

The reintroduction of the Eastern Migratory Population of Whooping Cranes ( Grus americana ) has shown the most promise of any effort to date toward the establishment of a self-sustaining population. However, reproduction – including both nest success and chick survival – has been a major challenge. Here, we review the research and management efforts deployed to identify and address this challenge. While there is evidence that a proximal cause of nest failure is harassment by blood-feeding black flies ( Simulium spp. ), this is not likely to be the only contributing factor, and we present alternative hypotheses. There is less understanding of the causes of poor chick survival, and we present hypotheses for factors that may be contributing to chick mortality, including environmental, genetic, and behavioral factors. For both nest success and chick survival, we carried out a value of information analysis, using expert judgment, which allowed us to prioritize the alternative hypotheses for evaluation based on the expected management benefit of addressing each hypothesis. On the horizon are multiple opportunities to explore hypotheses about environmental factors as well as genetic and behavioral characteristics of the birds themselves that may contribute to poor reproduction. If bird-specific characteristics, such as genetics or rearing methods, are hindering reproduction, this has important implications for all efforts to restore Whooping Crane populations.

Book chapter↗

USGS2018

Habitat mosaics and path analysis can improve biological conservation of aquatic biodiversity in ecosystems with low-head dams

Conserving native biodiversity depends on restoring functional habitats in the face of human-induced disturbances. Low-head dams are a ubiquitous human impact that degrades aquatic ecosystems worldwide. To improve our understanding of how low-head dams impact habitat and associated biodiversity, our research examined complex interactions among three spheres of the total environment. i.e., how low-head dams ( anthroposphere ) affect aquatic habitat ( hydrosphere ), and native biodiversity ( biosphere ) in streams and rivers. Creation of lake-like habitats upstream of low-head dams is a well-documented major impact of dams. Alterations downstream of low head dams also have important consequences, but these downstream dam effects are more challenging to detect. In a multidisciplinary field study at five dammed and five undammed sites within the Neosho River basin, KS, we tested hypotheses about two types of habitat sampling (transect and mosaic) and two types of statistical analyses (analysis of covariance and path analysis). We used fish as our example of biodiversity alteration. Our research provided three insights that can aid environmental professionals who seek to conserve and restore fish biodiversity in aquatic ecosystems threatened by human modifications. First, a mosaic approach identified habitat alterations below low-head dams (e.g. increased proportion of riffles) that were not detected using the more commonly-used transect sampling approach. Second, the habitat mosaic approach illustrated how low-head dams reduced natural variation in stream habitat. Third, path analysis, a statistical approach that tests indirect effects, showed how dams, habitat, and fish biodiversity interact. Specifically, path analysis revealed that low-head dams increased the proportion of riffle habitat below dams, and, as a result, indirectly increased fish species richness . Furthermore, the pool habitat that was created above low-head dams dramatically decreased fish species richness. As we show here, mosaic habitat sampling and path analysis can help conservation practitioners improve science-based management plans for disturbed aquatic systems worldwide.

Kansas↗

USGS2012

Classifications for Coastal Wetlands Planning, Protection and Restoration Act site-specific projects: 2008 and 2009

The Coastal Wetlands Planning, Protection and Restoration Act (CWPPRA) funds over 100 wetland restoration projects across Louisiana. Integral to the success of CWPPRA is its long-term monitoring program, which enables State and Federal agencies to determine the effectiveness of each restoration effort. One component of this monitoring program is the analysis of high-resolution, color-infrared aerial photography at the U.S. Geological Survey's National Wetlands Research Center in Lafayette, Louisiana. Color-infrared aerial photography (9- by 9-inch) is obtained before project construction and several times after construction. Each frame is scanned on a photogrametric scanner that produces a high-resolution image in Tagged Image File Format (TIFF). By using image-processing software, these TIFF files are then orthorectified and mosaicked to produce a seamless image of a project area and its associated reference area (a control site near the project that has common environmental features, such as marsh type, soil types, and water salinities.) The project and reference areas are then classified according to pixel value into two distinct classes, land and water. After initial land and water ratios have been established by using photography obtained before and after project construction, subsequent comparisons can be made over time to determine land-water change. Several challenges are associated with the land-water interpretation process. Primarily, land-water classifications are often complicated by the presence of floating aquatic vegetation that occurs throughout the freshwater systems of coastal Louisiana and that is sometimes difficult to differentiate from emergent marsh. Other challenges include tidal fluctuations and water movement from strong winds, which may result in flooding and inundation of emergent marsh during certain conditions. Compensating for these events is difficult but possible by using other sources of imagery to verify marsh conditions for other dates in time.

Louisiana↗

USGS2010

Background and introduction: Chapter 1

The Salt Cedar and Russian Olive Control Demonstration Act of 2006 (Public Law 109-320; hereafter the Act) directs the Department of the Interior to submit a report to Congress1 that includes an assessment of several issues surrounding these two nonnative trees, now dominant components of the vegetation along many rivers in the Western United States. Specifically, the Act calls for “…an assessment of the extent of salt cedar and Russian olive infestation on public and private land in the western United States,” which shall “A) consider existing research on methods to control salt cedar and Russian olive trees; B) consider the feasibility of reducing water consumption by salt cedar and Russian olive trees; C) consider methods of and challenges associated with the revegetation or restoration of infested land; and D) estimate the costs of destruction of salt cedar and Russian olive trees, related biomass removal, and revegetation or restoration and maintenance of the infested land.” Finally, the Act calls for discussion of “(i) long-term management and funding strategies…that could be implemented by Federal, State, tribal, and private land managers and owners to address the infestation by salt cedar and Russian olive; (ii) any deficiencies in the assessment or areas for additional study; and (iii) any field demonstrations that would be useful in the effort to control salt cedar and Russian olive.” The primary intent of this report is to provide the science assessment called for under the Act. A secondary purpose is to provide a common background for applicants for prospective demonstration projects, should funds be appropriated for this second phase of the Act. In addition to relying on the direction provided under Section C of the Act, the authors of this report also drew upon the detailed list of considerations presented in Section E of the Act to guide development of more expansive discussions of topics relevant to saltcedar and Russian olive control efforts. In addition to the legislative context described above, this chapter describes the geographic and environmental contexts surrounding the Act, including key terminology used in subsequent chapters of this report. Subsequent chapters synthesize the state-of-the-science on the following topics: distribution and abundance (extent) of saltcedar and Russian olive in the Western United States, potential for water savings associated with control of saltcedar and Russian olive and associated restoration, considerations related to wildlife use of saltcedar and Russian olive habitat or restored habitats, methods to control saltcedar and Russian olive, possible utilization of dead biomass following control, and approaches and challenges associated with revegetation or restoration following control. A concluding chapter includes discussion of possible long-term management strategies, areas for additional study, potentially useful field demonstrations, and a planning process for on-the-ground projects involving removal of saltcedar and Russian olive.

Book chapter↗

USGS2019

Brodifacoum toxicity in American Kestrels (Falco sparverius) with evidence of increased hazard upon subsequent anticoagulant rodenticide exposure

A seminal question in ecotoxicology is the extent to which contaminant exposure evokes prolonged effects on physiological function and fitness. A series of studies were undertaken with American kestrels ingesting environmentally realistic concentrations of the second-generation anticoagulant rodenticide (SGAR) brodifacoum (BROD). Kestrels fed BROD at 0.3, 1.0 or 3.0 µg/g diet wet wt for 7 d exhibited dose-dependent hemorrhage, histopathological lesions and coagulopathy (prolonged prothrombin and Russell’s viper venom times). Following termination of a 7 d exposure to 0.5 µg BROD/g diet, prolonged blood clotting time returned to baseline values within a week, but BROD residues in liver and kidney (terminal half-life estimates >50 d) persisted during the 28 d recovery period. In order to examine the hazard of sequential AR exposure, kestrels were exposed to either the firstgeneration AR chlorophacinone (CPN; 1.5 µg/g diet) or the SGAR BROD (0.5 µg/g diet) for 7 d, and following a recovery period, were challenged with a low dose of CPN (0.75 µg/g diet) for 7 d. In BROD-exposed kestrels, the challenge exposure clearly prolonged prothrombin time compared to naïve controls and kestrels previously exposed to CPN. These data provide evidence that the SGAR BROD may have prolonged effects that increase toxicity of subsequent AR exposure. As free-ranging predatory and scavenging wildlife are often repeatedly exposed to ARs, such protracted toxicological effects need to be considered in hazard and risk assessments.

Environmental Toxicology and Chemistry↗

USGS2022

Special section overview: Effects of ecosystem change on North American percid populations.

Walleye Sander vitreus , Sauger S. canadensis , and Yellow Perch Perca flavescens (referred to as percids herein) are collectively among the most culturally and ecologically important fish species in North America. As ecosystems change in response to environmental drivers, such as climate change, nutrient loading, and invasive species, there is a need to understand how percid populations respond to these changes. To address this need, a symposium was held during the 81st Annual Midwest Fish and Wildlife Conference to bring fishery scientists and managers together to describe and discuss percid population responses to ecosystem change. Prevailing symposium themes included the challenge of identifying mechanisms responsible for population-level changes, developing strategies to adaptively manage for resilient fisheries, and consideration of scale, context, and methods when interpreting variable results. Given the uncertainty of how ecosystem changes affect percid populations, participants emphasized the importance of communicating uncertainties to stakeholders, implementing data-driven management strategies, setting realistic goals, and revising management actions in an adaptive framework. There was universal agreement on both the challenge and necessity of facilitating constructive engagement among stakeholders in cooperative decision making. Symposium participants identified knowledge gaps and discussed future efforts to build on our current understanding of percid populations, including continuation of long-term monitoring, improved standardization of evaluation metrics, implementing adaptive management experiments to identify causal relationships, development of more robust analytical methods, use of historical data sources, and refining techniques to realistically convey management options to stakeholders.

North American Journal of Fisheries Management↗

USGS2020

Conservation genomics in a changing arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Trends in Ecology and Evolution↗

USGS2006

Adaptive harvest management of North American waterfowl populations - recent successes and future prospects

The history of North American waterfowl harvest management has been characterized by attempts to use population monitoring data to make informed harvest management decisions. Early attempts can be characterized as intuitive decision processes, and later efforts were guided increasingly by population models and associated predictions. In 1995, a formal adaptive management process was implemented, and annual decisions about duck harvest regulations in the United States are still based on this process. This formal decision process is designed to deal appropriately with the various forms of uncertainty that characterize management decisions, environmental uncertainty, structural uncertainty, partial controllability and partial observability. The key components of the process are (1) objectives, (2) potential management actions, (3) model(s) of population response to management actions, (4) credibility measures for these models, and (5) a monitoring program. The operation of this iterative process is described, and a brief history of a decade of its use is presented. Future challenges range from social and political issues such as appropriate objectives and management actions, to technical issues such as multispecies management, geographic allocation of harvest, and incorporation of actions that include habitat acquisition and management.

Book chapter↗