Geology ReportsSearch

SEARCH · Geology Reports

Results for “Environmental Conservation”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 505 records · Page 28Linked to original sources

Ecosystem services: developing sustainable management paradigms based on wetland functions and processes

In the late nineteenth century and twentieth century, there was considerable interest and activity to develop the United States for agricultural, mining, and many other purposes to improve the quality of human life standards and prosperity. Most of the work to support this development was focused along disciplinary lines with little attention focused on ecosystem service trade-offs or synergisms, especially those that transcended boundaries of scientific disciplines and specific interest groups. Concurrently, human population size has increased substantially and its use of ecosystem services has increased more than five-fold over just the past century. Consequently, the contemporary landscape has been highly modified for human use, leaving behind a fragmented landscape where basic ecosystem functions and processes have been broadly altered. Over this period, climate change also interacted with other anthropogenic effects, resulting in modern environmental problems having a complexity that is without historical precedent. The challenge before the scientific community is to develop new science paradigms that integrate relevant scientific disciplines to properly frame and evaluate modern environmental problems in a systems-type approach to better inform the decision-making process. Wetland science is a relatively new discipline that grew out of the conservation movement of the early twentieth century. In the United States, most of the conservation attention in the earlier days was on wildlife, but a growing human awareness of the importance of the environment led to the passage of the National Environmental Policy Act in 1969. Concurrently, there was a broadening interest in conservation science, and the scientific study of wetlands gradually gained acceptance as a scientific discipline. Pioneering wetland scientists became formally organized when they formed The Society of Wetland Scientists in 1980 and established a publication outlet to share wetland research findings. In comparison to older and more traditional scientific disciplines, the wetland sciences may be better equipped to tackle today’s complex problems. Since its emergence as a scientific discipline, the study of wetlands has frequently required interdisciplinary and integrated approaches. This interdisciplinary/integrated approach is largely the result of the fact that wetlands cannot be studied in isolation of upland areas that contribute surface and subsurface water, solutes, sediments, and nutrients into wetland basins. However, challenges still remain in thoroughly integrating the wetland sciences with scientific disciplines involved in upland studies, especially those involved with agriculture, development, and other land-conversion activities that influence wetland hydrology, chemistry, and sedimentation. One way to facilitate this integration is to develop an understanding of how human activities affect wetland ecosystem services, especially the trade-offs and synergisms that occur when land-use changes are made. Used in this context, an understanding of the real costs of managing for a particular ecosystem service or groups of services can be determined and quantified in terms of reduced delivery of other services and in overall sustainability of the wetland and the landscapes that support them. In this chapter, we discuss some of the more salient aspects of a few common wetland types to give the reader some background on the diversity of functions that wetlands perform and the specific ecosystem services they provide to society. Wetlands are among the most complex ecosystems on the planet, and it is often difficult to communicate to a diverse public all of the positive services wetlands provide to mankind. Our goal is to help the reader develop an understanding that management options can be approached as societal choices where decisions can be made within a spatial and temporal context to identify trade-offs, synergies, and effects on long-term sustainability of wetland ecosystems. This will be especially relevant as we move into alternate climate futures where our portfolio of management options for mitigating damage to ecosystem function or detrimental cascading effects must be diverse and effective.

Book chapter

Movers and stayers: Novel assemblages in changing environments

How species will respond to ongoing climate and other change is of increasing concern. Most attention is given to how species move or are moved, but many species stay. Understanding the dynamics of new species combinations is essential for successful conservation in a changing climate. Increased attention to species movement in response to environmental change highlights the need to consider changes in species distributions and altered biological assemblages. Such changes are well known from paleoecological studies, but have accelerated with ongoing pervasive human influence. In addition to species that move, some species will stay put, leading to an array of novel interactions. Species show a variety of responses that can allow movement or persistence. Conservation and restoration actions have traditionally focused on maintaining or returning species in particular places, but increasingly also include interventions that facilitate movement. Approaches are required that incorporate the fluidity of biotic assemblages into the goals set and interventions deployed.

Trends in Ecology and Evolution

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

AIMS for wildlife: Developing an automated interactive monitoring system to integrate real-time movement and environmental data for true adaptive management

To effectively manage species and habitats at multiple scales, population and land managers require rapid information on wildlife use of managed areas and responses to landscape conditions and management actions. GPS tracking studies of wildlife are particularly informative to species ecology, habitat use, and conservation. Combining GPS data with administrative data and a diverse suite of remotely sensed, geo-referenced environmental (e.g., climatic) data, would more comprehensively inform how animals interact with and utilize habitats and ecosystems and our goal was to create a conceptual model for a system that would accomplish this – the ‘Automated Interactive Monitoring System (AIMS) for Wildlife’. Our objective for this study was to develop a Customized Wildlife Report (CWR) - the first AIMS for Wildlife deliverable product. CWRs collate and summarize our 8-year GPS tracking dataset of ∼11 million locations from 1338 individual (16 species) avifauna and make actionable, real-time data on animal movements and trends in a specific area of interest available to managers and stakeholders for rapid application in day-to-day management. The CWR exemplar presented in this paper was developed to address needs identified by habitat managers of Sacramento National Wildlife Refuge and illustrates the highly specific, information offered and how it contributes to assessing the efficacy of conservation actions while allowing for near real-time adaptive management. The report can be easily customized for any of the thousands of wildlife refuges or regional areas of interest in the United States, emphasizing the broad application of an animal movement data stream. Utilizing diverse, extensive telemetry data streams through scientific collaboration can aid managers and conservation stakeholders with short and long-term research and conservation planning and help address a cadre of issues from local-scale habitat management to improving the understanding of landscape level impacts like drought, wildfire, and climate change on wildlife populations.

Journal of Environmental Management

Mobile Bay

Mobile Bay is the largest bay found in Alabama’s coastal area (Handley et al., 2007). It was named an Estuary of National Significance in 1995 under the U.S. Environmental Protection Agency’s (EPA) National Estuary Program (NEP), and its Comprehensive Conservation Management Plan was completed in 2002. Mobile Bay is 1,070 km 2 (413 miles 2 ) in area and 51 km (32 miles) long, making it the sixth largest estuary in the continental United States (Mobile Bay NEP, 2008). Its ecosystem provides habitat for more than 300 species of birds, 310 species of fish, 68 species of reptiles, 57 species of mammals, 40 species of amphibians, and 15 species of shrimp (Mobile Bay NEP, 1997). Mobile Bay lies between the Mississippi and Atlantic Flyways (Mobile Bay NEP, 2003). Commercial and residential development and industrial use is heavy in the Mobile Bay area. Although local growth and industrial markets support the Mobile Bay area economy, the resulting environmental damage to the very ecosystem upon which they depend remains a threat to the environment, economy, and population. The Mobile Bay ecosystem boasts high biological diversity and productivity and supports many freshwater and saltwater species of recreational and commercial importance. The great diversity of Mobile Bay reflects the diversity of Alabama, which is home to the largest number of different plant and animal species of all states east of the Mississippi River (Stein, 2002), and is bolstered by the unique climate and geographic conditions surrounding the bay. Freshwater inflow from the Mobile-Tensaw River Delta, ranging from 60,000 to 3,700,000 gallons per second (Wallace, 1996), mixes with saltwater from the Gulf of Mexico, which enters Mobile Bay via wind and tides (Burgan and Engle, 2006). Because of the unique conditions surrounding Mobile Bay, including shallow waters, a dynamic climate, and artificial hydrologic modifications—such as the construction of the Mobile Bay Causeway in the 1920s, which serves as an unintentional barrier between Delta waters north of the Causeway and saline waters south of the Causeway, the salinity of Mobile Bay is highly variable. Mobile Bay receives an average of 165 cm (65 inches) of rain per year from tropical storms, summer thunderstorms, and winter cold fronts (Stout et al., 1998). The climate and geography that have made Mobile Bay so rich in resources have also contributed to the threats surrounding its ecosystem. The extensive amount of rain in Mobile Bay creates large amounts of runoff, polluting the waters with fertilizers, chemicals, sediment, oil, trash, and sewage (Mobile Bay NEP, 1997). Tourism, ecotourism, recreational and commercial fishing, recreational boating, shipping, and chemical, pulp, and paper production are significant industries in Mobile Bay and the surrounding areas. Despite the approximate \$3 billion and 55,000 jobs these industries bring into the community (Alabama Tourism Department, 2010), the growth, development, and environmental stress they create are major threats to the Mobile Bay ecosystem. Among the nation’s states, Alabama ranks fifth in number of different species (144 endemic species), second in number of extinctions that have already occurred (90 extinct species) and fourth in number of species at risk for extinction (14.8% at risk out of 4,533 total species; Stein, 2002). Twenty-one of these threatened and endangered species are found in Mobile Bay, whose brackish waters provide a nursery area for many species of vertebrates and invertebrates. Some of these species include the Alabama sturgeon, Gulf sturgeon, heavy pigtoe mussel, inflated heel-splitter mussel, West Indian manatee, Alabama beach mouse, Perdido beach mouse, Alabama red-bellied turtle, gopher tortoise, Kemp’s ridley sea turtle, green sea turtle, loggerhead sea turtle, eastern indigo snake, flatwoods salamander, piping plover, red-cockaded woodpecker, and wood stork. Habitat loss underlies the decline of some bird species in Mobile Bay, and large mammals such as the red wolf, Florida panther, and Florida black bear are no longer found in the area. However, some rare species, such as the swallow-tailed kite, sandhill crane, and gopher tortoise can still be found (Duke and Kruczynski, 1992). The value of wetlands in Mobile Bay and the rest of the Gulf of Mexico is still being investigated. Although various monetary valuations of wetlands exist, critics remark that undervaluation of wetlands is inevitable (Mobile Bay NEP, 2008) and that estimates often do not place appropriate value on ecological services (Mitsch and Gosselink, 2000). Additionally, many estimates account only for anthropogenic values. One estimate concludes that one acre of wetlands performs \$3,000 worth of water purification each year (Mobile Bay NEP, 1997). With more than 76,890 hectares (190,000 acres) of wetlands in the Mobile Bay area, that equates to a value exceeding one-half billion dollars every year. Tourism, fishing, boating, production, and shipping are significant industries in the Mobile Bay area. More than 90% of fish landed in recreational and commercial fishing in the bay depend on bay habitat, including wetlands, for life requirements (Mobile Bay NEP, 1997). The Port of Mobile is Alabama’s only ocean-ship port (Mobile Bay NEP, 2008). Baldwin County, on the eastern side of the bay, experienced a population increase of 75% from 1990 to 2007, with an 89% increase in housing units (Mobile Bay NEP, 2008). Development and industry support the Mobile Bay economy, but they depend on the continued health, sustainability, and production of the water and living resources of the Mobile Bay ecosystem. Wetland loss, along with other forms of environmental degradation, remains a threat to the Mobile Bay ecosystem and Mobile Bay’s socioeconomic foundation.

Alabama

Endangered river fish: factors hindering conservation and restoration

Globally, riverine fish face many anthropogenic threats including riparian and flood plain habitat degradation, altered hydrology, migration barriers, fisheries exploitation, environmental (climate) change, and introduction of invasive species. Collectively, these threats have made riverine fishes some of the most threatened taxa on the planet. Although much effort has been devoted to identifying the threats faced by river fish, there has been less effort devoted to identifying the factors that may hinder our ability to conserve and restore river fish populations and their watersheds. Therefore, we focus our efforts on identifying and discussing 10 general factors (can also be viewed as research and implementation needs) that constrain or hinder effective conservation action for endangered river fish: (1) limited basic natural history information; (2) limited appreciation for the scale/extent of migrations and the level of connectivity needed to sustain populations; (3) limited understanding of fish/river-flow relationships; (4) limited understanding of the seasonal aspects of river fish biology, particularly during winter and/or wet seasons; (5) challenges in predicting the response of river fish and river ecosystems to both environmental change and various restoration or management actions; (6) limited understanding of the ecosystem services provided by river fish; (7) the inherent difficulty in studying river fish; (8) limited understanding of the human dimension of river fish conservation and management; (9) limitations of single species approaches that often fail to address the broader-scale problems; and (10) limited effectiveness of governance structures that address endangered river fish populations and rivers that cross multiple jurisdictions. We suggest that these issues may need to be addressed to help protect, restore, or conserve river fish globally, particularly those that are endangered.

Endangered Species Research

Decadal stability in stream fish communities and contemporary ecological drivers of species occupancy in two Appalachian U.S. National Parks

Objective Although conserving fish biodiversity in lotic systems is challenging, protected areas can provide refuge from certain environmental stressors. In the Appalachian region, USA, the National Park Service manages Delaware Water Gap National Recreation Area (DEWA) and New River Gorge National Park & Preserve (NERI), which contain abundant and diverse freshwater resources. To assess the effectiveness of these protected areas in conserving stream fishes, we evaluated decadal changes and ecological drivers of species occupancy and detection. Methods Using fish assemblage data from backpack electrofishing surveys conducted in both parks during 2013–2014 and 2022–2023, we quantified temporal differences in species occupancy and detection probabilities using a Bayesian hierarchical multispecies occupancy modeling approach. For the 2022–2023 survey, we included habitat variables as predictors of occupancy and detection. Results Community composition and occupancy probabilities for species in both parks remained similar through time, with the most recent occupancy estimates ranging from 0.07 (90% CI = 0.02, 0.14) for Variegate Darter Etheostoma variatum and Rainbow Darter E. ­caeruleum to 0.73 (90% credible interval = 0.59, 0.85) for Blacknose Dace Rhinichthys atratulus . Changes in occupancy were more prominent at Delaware Water Gap National Recreation Area than New River Gorge National Park & Preserve, with Yellow Perch Perca flavescens having a posterior mean difference of −0.17 [90% credible interval = −0.35, −0.01] and American Eel Anguilla rostrata having a high posterior probability (>80%) of occupancy increasing by at least 1%. Habitat variables were related to community structure, but effects varied in significance, magnitude, and direction among species and parks. Conversely, species-specific detection probabilities were comparatively less affected by environmental and sampling effort predictors. Conclusions Between 2013 and 2023, occupancy estimates for 44 fish species across two protected, ecologically diverse landscapes remained relatively stable. Furthermore, we highlight the efficacy of national parks in maintaining freshwater fish biodiversity amidst rapid global change.

New Jersey, Pennsylvania, West Virginia

Linking evolutionary potential to extinction risk: Applications and future directions

Extinction-risk assessments play a major role in prioritizing conservation action at national and international levels. However, quantifying extinction risk is challenging, especially when including the full suite of adaptive responses to environmental change. In particular, evolutionary potential (EP), the capacity to evolve genetically based changes that increase fitness under changing conditions, has proven difficult to evaluate, limiting its inclusion in risk assessments. Theory, experiments, simulations, and field studies all highlight the importance of EP in characterizing and mitigating extinction risk. Disregarding EP can therefore result in ineffective allocation of resources and inadequate recovery planning. Fortunately, proxies for EP can be estimated from environmental, phenotypic, and genetic data. Some proxies can be incorporated into quantitative extinction-risk assessments, whereas others better inform basic conservation actions that maximize resilience to future change. Integration of EP into conservation decision-making is challenging but essential and remains an important area for innovation in applied conservation science.

Frontiers in Ecology and the Environment

Cisco population characteristics in Wisconsin lakes in relation to lake- and landscape-level factors

Objective Declines in Cisco Coregonus artedi populations in some inland lakes have prompted assessments of Cisco occurrence and extirpation risk in relation to various stressors to identify refuge lakes and factors that promote Cisco persistence. However, most previous assessments have focused on presence–absence of Cisco rather than examining how population characteristics, such as relative abundance or growth, might change in relation to lake- and landscape-level environmental factors. Consequently, our specific objectives were to identify important environmental factors explaining variation in Cisco relative abundance and growth and to determine whether population metrics describing size and age distributions were related to relative abundance in Wisconsin inland lakes. Methods Cisco were collected from 48 inland Wisconsin lakes during 2011–2015 using vertical monofilament gill nets and population-specific relative abundance estimates (catch per unit effort [CPUE]) were quantified as the number of individuals per gill-net night. Sagittal otoliths were removed from a subsample of Cisco for age estimation and growth was indexed as mean total length (TL; mm) at age 2. Length and age data were used to develop a suite of metrics describing size and age distributions of each population. Random forest models were used to evaluate relationships between 10 biologically relevant predictor variables representing variation in physical, climatic, catchment, and limnological characteristics and Cisco CPUE and growth. Pearson correlations were used to determine whether population characteristics were related to CPUE. Result Cisco populations exhibited large variation in relative abundance, growth, and size and age distributions. Best-fit random forest models explained approximately 25% of the variation in Cisco CPUE and 46% of the variation in growth. Growing degree-days and variables associated with availability, quality, and quantity of suitable oxythermal conditions were identified as important predictors of both Cisco CPUE and growth; CPUE was also identified as an important predictor of growth. Mean TL and mean TL at age 2 were negatively related to Cisco CPUE, whereas mean age, number of age-classes present, and maximum observed age were positively related to CPUE. Conclusion Our results suggest that maintenance of suitable oxythermal habitat conditions may be critical to conserving abundant Cisco populations. Our assessment also provides insights on how Cisco populations may respond to environmental and anthropogenic stressors, which could aid ongoing and future conservation and management efforts in Wisconsin and elsewhere.

Wisconsin

Contemporary spatial extent and environmental drivers of larval coregonine distributions across Lake Ontario

Coregonine fishes are important to Laurentian Great Lakes food webs and fisheries and are central to basin-wide conservation initiatives. In Lake Ontario, binational management objectives include conserving and restoring spawning stocks of cisco ( Coregonus artedi ) and lake whitefish ( C. clupeaformis ), but the spatial extent of contemporary coregonine spawning habitat and the environmental factors regulating early life success are not well characterized. In Spring 2018, we conducted a binational ichthyoplankton assessment to describe the spatial extent of coregonine spawning habitat across Lake Ontario. We then quantified the relative importance of a suite of biophysical variables hypothesized to influence coregonine early life success using generalized additive mixed models and multimodel inference. Between April 10 and May 14, we conducted 1,092 ichthyoplankton tows and captured 2,350+ coregonine larvae across 17 sampling areas, predominantly within embayments. Although 95% of catches were in the eastern basin, coregonine larvae were also found in historical south shore spawning areas. Most coregonine larvae were cisco; <6% were lake whitefish. Observed catches of both species across sampling areas were strongly and similarly associated with ice cover duration, but the importance of site-specific characteristics varied, such as distance to shore and site depth for cisco and lake whitefish, respectively. These results suggest that regional-scale climatic drivers and local environmental habitat characteristics interact to regulate early life stage success. Furthermore, strong regional and cross-species variation in larval distributions emphasize the importance of lake-wide assessments for monitoring both the current eastern basin populations and potential expansions into western Lake Ontario habitats.

Lake Ontario

Topographic and fire weather controls of fire refugia in forested ecosystems of northwestern North America

Fire refugia, sometimes referred to as fire islands, shadows, skips, residuals, or fire remnants, are an important element of the burn mosaic, but we lack a quantitative framework that links observations of fire refugia from different environmental contexts. Here, we develop and test a conceptual model for how predictability of fire refugia varies according to topographic complexity and fire weather conditions. Refugia were quantified as areas unburned or burned at comparatively low severity based on remotely sensed burn severity data. We assessed the relationship between refugia and a suite of terrain-related explanatory metrics by fitting a collection of boosted regression tree models. The models were developed for seven study fires that burned in conifer-dominated forested landscapes of the Western Cordillera of Canada between 2001 and 2014. We fit nine models, each for distinct levels of fire weather and terrain ruggedness. Our framework revealed that the predictability and abundance of fire refugia varied among these environmental settings. We observed highest predictability under moderate fire weather conditions and moderate terrain ruggedness (ROC-AUC = 0.77), and lowest predictability in flatter landscapes and under high fire weather conditions (ROC-AUC = 0.63–0.68). Catchment slope, local aspect, relative position, topographic wetness, topographic convergence, and local slope all contributed to discriminating where refugia occur but the relative importance of these topographic controls differed among environments. Our framework allows us to characterize the predictability of contemporary fire refugia across multiple environmental settings and provides important insights for ecosystem resilience, wildfire management, conservation planning, and climate change adaptation.

Ecosphere

Moving environmental DNA methods from concept to practice for monitoring aquatic macroorganisms

The discovery that macroorganisms can be detected from their environmental DNA (eDNA) in aquatic systems has immense potential for the conservation of biological diversity. This special issue contains 11 papers that review and advance the field of eDNA detection of vertebrates and other macroorganisms, including studies of eDNA production, transport, and degradation; sample collection and processing to maximize detection rates; and applications of eDNA for conservation using citizen scientists. This body of work is an important contribution to the ongoing efforts to take eDNA detection of macroorganisms from technical breakthrough to established, reliable method that can be used in survey, monitoring, and research applications worldwide. While the rapid advances in this field are remarkable, important challenges remain, including consensus on best practices for collection and analysis, understanding of eDNA diffusion and transport, and avoidance of inhibition in sample collection and processing. Nonetheless, as demonstrated in this special issue, eDNA techniques for research and monitoring are beginning to realize their potential for contributing to the conservation of biodiversity globally.

Biological Conservation

Sustainable water management under future uncertainty with eco-engineering decision scaling

Managing freshwater resources sustainably under future climatic and hydrological uncertainty poses novel challenges. Rehabilitation of ageing infrastructure and construction of new dams are widely viewed as solutions to diminish climate risk, but attaining the broad goal of freshwater sustainability will require expansion of the prevailing water resources management paradigm beyond narrow economic criteria to include socially valued ecosystem functions and services. We introduce a new decision framework, eco-engineering decision scaling (EEDS), that explicitly and quantitatively explores trade-offs in stakeholder-defined engineering and ecological performance metrics across a range of possible management actions under unknown future hydrological and climate states. We illustrate its potential application through a hypothetical case study of the Iowa River, USA. EEDS holds promise as a powerful framework for operationalizing freshwater sustainability under future hydrological uncertainty by fostering collaboration across historically conflicting perspectives of water resource engineering and river conservation ecology to design and operate water infrastructure for social and environmental benefits.

Nature Climate Change

Reconstructing population dynamics of a threatened marine mammal using multiple data sets

Models of marine mammal population dynamics have been used extensively to predict abundance. A less common application of these models is to reconstruct historical population dynamics, filling in gaps in observation data by integrating information from multiple sources. We developed an integrated population model for the Florida manatee ( Trichechus manatus latirostris ) to reconstruct its population dynamics in the southwest region of the state over the past 20 years. Our model improved precision of key parameter estimates and permitted inference on poorly known parameters. Population growth was slow (averaging 1.02; 95% credible interval 1.01–1.03) but not steady, and an unusual mortality event in 2013 led to an estimated net loss of 332 (217–466) manatees. Our analyses showed that precise estimates of abundance could be derived from estimates of vital rates and a few input estimates of abundance, which may mean costly surveys to estimate abundance don’t need to be conducted as frequently. Our study also shows that retrospective analyses can be useful to: (1) model the transient dynamics of age distribution; (2) assess and communicate the conservation status of wild populations; and (3) improve our understanding of environmental effects on population dynamics and thus enhance our ability to forecast.

Florida

A benchmark for computational analysis of animal behavior, using animal-borne tags

Background Animal-borne sensors (‘bio-loggers’) can record a suite of kinematic and environmental data, which are used to elucidate animal ecophysiology and improve conservation efforts. Machine learning techniques are used for interpreting the large amounts of data recorded by bio-loggers, but there exists no common framework for comparing the different machine learning techniques in this domain. This makes it difficult to, for example, identify patterns in what works well for machine learning-based analysis of bio-logger data. It also makes it difficult to evaluate the effectiveness of novel methods developed by the machine learning community. Methods To address this, we present the Bio-logger Ethogram Benchmark (BEBE), a collection of datasets with behavioral annotations, as well as a modeling task and evaluation metrics. BEBE is to date the largest, most taxonomically diverse, publicly available benchmark of this type, and includes 1654 h of data collected from 149 individuals across nine taxa. Using BEBE, we compare the performance of deep and classical machine learning methods for identifying animal behaviors based on bio-logger data. As an example usage of BEBE, we test an approach based on self-supervised learning. To apply this approach to animal behavior classification, we adapt a deep neural network pre-trained with 700,000 h of data collected from human wrist-worn accelerometers. Results We find that deep neural networks out-perform the classical machine learning methods we tested across all nine datasets in BEBE. We additionally find that the approach based on self-supervised learning out-performs the alternatives we tested, especially in settings when there is a low amount of training data available. Conclusions In light of these results, we are able to make concrete suggestions for designing studies that rely on machine learning to infer behavior from bio-logger data. Therefore, we expect that BEBE will be useful for making similar suggestions in the future, as additional hypotheses about machine learning techniques are tested. Datasets, models, and evaluation code are made publicly available at https://github.com/earthspecies/BEBE , to enable community use of BEBE.

Movement Ecology

Simulation of effects of wastewater discharges on Sand Creek and lower Caddo Creek near Ardmore, Oklahoma

A streamflow and water-quality model was developed for reaches of Sand and Caddo Creeks in south-central Oklahoma to simulate the effects of wastewater discharge from a refinery and a municipal treatment plant. The purpose of the model was to simulate conditions during low streamflow when the conditions controlling dissolved-oxygen concentrations are most severe. Data collected to calibrate and verify the streamflow and water-quality model include continuously monitored streamflow and water-quality data at two gaging stations and three temporary monitoring stations; wastewater discharge from two wastewater plants; two sets each of five water-quality samples at nine sites during a 24-hour period; dye and propane samples; periphyton samples; and sediment oxygen demand measurements. The water-quality sampling, at a 6-hour frequency, was based on a Lagrangian reference frame in which the same volume of water was sampled at each site. To represent the unsteady streamflows and the dynamic water-quality conditions, a transport modeling system was used that included both a model to route streamflow and a model to transport dissolved conservative constituents with linkage to reaction kinetics similar to the U.S. Environmental Protection Agency QUAL2E model to simulate nonconservative constituents. These model codes are the Diffusion Analogy Streamflow Routing Model (DAFLOW) and the branched Lagrangian transport model (BLTM) and BLTM/QUAL2E that, collectively, as calibrated models, are referred to as the Ardmore Water-Quality Model. The Ardmore DAFLOW model was calibrated with three sets of streamflows that collectively ranged from 16 to 3,456 cubic feet per second. The model uses only one set of calibrated coefficients and exponents to simulate streamflow over this range. The Ardmore BLTM was calibrated for transport by simulating dye concentrations collected during a tracer study when streamflows ranged from 16 to 23 cubic feet per second. Therefore, the model is expected to be most useful for low streamflow simulations. The Ardmore BLTM/QUAL2E model was calibrated and verified with water-quality data from nine sites where two sets of five samples were collected. The streamflow during the water-quality sampling in Caddo Creek at site 7 ranged from 8.4 to 20 cubic feet per second, of which about 5.0 to 9.7 cubic feet per second was contributed by Sand Creek. The model simulates the fate and transport of 10 water-quality constituents. The model was verified by running it using data that were not used in calibration; only phytoplankton were not verified. Measured and simulated concentrations of dissolved oxygen exhibited a marked daily pattern that was attributable to waste loading and algal activity. Dissolved-oxygen measurements during this study and simulated dissolved-oxygen concentrations using the Ardmore Water-Quality Model, for the conditions of this study, illustrate that the dissolved-oxygen sag curve caused by the upstream wastewater discharges is confined to Sand Creek.

Water-Resources Investigations Report

Predicting regional abundance of rare grassland birds with a hierarchical spatial count model

Grassland birds are among the most imperiled groups of birds in North America. Unfortunately, little is known about the location of regional concentrations of these birds, thus regional or statewide conservation efforts may be inappropriately applied, reducing their effectiveness. We identified environmental covariates associated with the abundance of five grassland birds in the upper midwestern United States (Bobolink [Dolichonyx oryzivorus], Grasshopper Sparrow [Ammodramus savannarum], Henslow's Sparrow [A. henslowii], Sedge Wren [Cistothorus platensis], and Upland Sandpiper [Bartramia longicauda]) with a hierarchical spatial count model fitted with Markov chain Monte Carlo methods. Markov chain Monte Carlo methods are well suited to this task because they are able to incorporate effects associated with autocorrelated counts and nuisance effects associated with years and observers, and the resulting models can be used to map predicted abundance at a landscape scale. Environmental covariates were derived from five suites of variables: landscape composition, landscape configuration, terrain heterogeneity and physiognomy, climate, and human influence. The final models largely conformed to our a priori expectations. Bobolinks and Henslow's Sparrows were strongly sensitive to grassland patch area. All of the species except Henslow's Sparrows exhibited substantial negative relations with forest composition, often at multiple spatial scales. Climate was found to be important for all species, and was the most important factor influencing abundance of Grasshopper Sparrows. After mapping predicted abundance, we found no obvious correspondence in the regional patterns of the five species. Thus, no clearly defined areas exist within the upper midwestern United States where management plans can be developed for a whole suite of grassland birds. Instead, a larger, region-wide initiative setting different goals for different species is recommended.

Condor

Differential exposure, duration, and sensitivity of unionoidean bivalve life stages to environmental contaminants

Freshwater mussels (superfamily Unionoidea) are in serious global decline and in urgent need of protection and conservation. The declines have been attributed to a wide array of human activities resulting in pollution and water-quality degradation, and habitat destruction and alteration. Linkages among poor water quality, pollutant sources, and mussel decline in rivers and streams have been associated with results of laboratory-based tests of specific pollutants. However, uncertainties remain about the relationship of laboratory data to actual contaminant exposure routes for various mussel species, life stages, and in the habitats occupied during these exposures. We evaluated the pathways of exposure to environmental pollutants for all 4 life stages (free glochidia, encysted glochidia, juveniles, adults) of unionoidean mussels and found that each life stage has both common and unique characteristics that contribute to observed differences in exposure and sensitivity. Free glochidia typically are exposed only briefly (e.g., seconds to days) through surface water, whereas adults sustain exposure over years to decades through surface water, pore water, sediment, and diet. Juveniles live largely burrowed in the sediment for the first 0 to 4 y of life. Thus, sediment, pore water, and diet are the predominant exposure routes for this life stage, but surface water also might contribute to exposure during certain periods and environmental conditions. The obligate parasitic stage (encysted glochidia stage) on a host fish might be exposed from surface water while partially encysted or from toxicants in host-fish tissue while fully encysted. Laboratory methods for testing for acute and chronic exposures in water have advanced, and toxicant-specific information has increased in recent years. However, additional research is needed to understand interactions of life history, habitat, and long-term exposure to contaminants through water, pore water, sediment, and diet so that the risks of environmental exposures can be properly assessed and managed. ?? 2008 by The North American Benthological Society.

Journal of the North American Benthological Societ