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USGS2004

Abundance estimation and conservation biology

Abundance is the state variable of interest in most population–level ecological research and in most programs involving management and conservation of animal populations. Abundance is the single parameter of interest in capture–recapture models for closed populations (e.g., Darroch, 1958; Otis et al., 1978; Chao, 2001). The initial capture–recapture models developed for partially (Darroch, 1959) and completely (Jolly, 1965; Seber, 1965) open populations represented efforts to relax the restrictive assumption of population closure for the purpose of estimating abundance. Subsequent emphases in capture–recapture work were on survival rate estimation in the 1970’s and 1980’s (e.g., Burnham et al., 1987; Lebreton et al.,1992), and on movement estimation in the 1990’s (Brownie et al., 1993; Schwarz et al., 1993). However, from the mid–1990’s until the present time, capture–recapture investigators have expressed a renewed interest in abundance and related parameters (Pradel, 1996; Schwarz & Arnason, 1996; Schwarz, 2001). The focus of this session was abundance, and presentations covered topics ranging from estimation of abundance and rate of change in abundance, to inferences about the demographic processes underlying changes in abundance, to occupancy as a surrogate of abundance. The plenary paper by Link & Barker (2004) is provocative and very interesting, and it contains a number of important messages and suggestions. Link & Barker (2004) emphasize that the increasing complexity of capture–recapture models has resulted in large numbers of parameters and that a challenge to ecologists is to extract ecological signals from this complexity. They offer hierarchical models as a natural approach to inference in which traditional parameters are viewed as realizations of stochastic processes. These processes are governed by hyperparameters, and the inferential approach focuses on these hyperparameters. Link & Barker (2004) also suggest that our attention should be focused on relationships between demographic processes such as survival and recruitment, the two quantities responsible for changes in abundance, rather than simply on the magnitudes of these quantities. They describe a type of Jolly–Seber capture–recapture model that permits inference about the underlying relationship between per capita recruitment rates and survival rates (Link & Barker, this volume). Implementation used Bayesian Markov Chain Monte Carlo methods and appeared to work well, yielding inferences about the relationship between recruitment and survival that were robust to selection of prior distribution. We believe that readers will find their arguments compelling, and we expect to see increased use of hierarchical modeling approaches in capture–recapture and related fields. Otto (presentation without paper) also recommended use of hierarchical models in analysis of multiple data sources dealing with population dynamics of North American mallards. He integrated survival inferences from ringing data, abundance information from aerial survey data, and recruitment information based on age ratios from a harvest survey. He used a Leslie matrix population projection model as an integrating framework and obtained estimates of breeding population size using all data.Otto’s approach also permitted inference about biases in estimated quantities. As with the work of Link & Barker (2004), we find Otto’s recommendation to use hierarchical models to integrate data from multiple sources to be very compelling. Alisauskas et al. (2004) report results of an analysis of capture–recapture data for a askatchewan population of white–winged scoters. They used the approach of Pradel (1996) to estimate population growth rate (See the PDF) directly. Estimates for 1975–1985 were quite low, but estimates for the recent period, 2000–2003,increased to values > 1. Parameter estimates for seniority, survival and per capita recruitment (Pradel, 1996) led to the inference that increased recruitment was largely responsible for the improvements in population status and growth. However, various data sources also indicated that this increase in recruitment was likely a result of increased immigration rather than improved reproduction on the area. This latter inference is important from a conservation perspective in indicating the importance of birds in other locations to growth and health of the study population. Lukacs and Burnham presented material to be published elsewhere that dealt with the use of genetic markers in capture–recapture studies. The data sources for such studies are samples of hair or feces, which are then analyzed using molecular genetic techniques in order to determine individual genotypes with respect to a usually small number of loci. Two types of classification error can arise in such analyses. First, if only a small number of loci is examined, then there may be nonnegligible probabilities that multiple individual animals will have the same genotypes. The second type of error arises during the polymerase chain reaction (PCR) process and can result from failure of alleles to amplify (allelic dropout) or from PCR inhibitors in hair and feces that produce the appearance of false alleles or misprinting (Creel et al., 2003). Lukacs and Burnham developed models that formally incorporate possible misclassification of samples resulting from these errors. These models permit estimation of parameters such as abundance and survival in a manner that properly incorporates this uncertainty of individual identity. We anticipate that noninvasive sampling based on molecular genetic analyses of hair or feces will become extremely important for some species, and that the models of Lukacs and Burnham will become very popular for such analyses. MacKenzie & Nichols (2004) discuss the use of occupancy (proportion of patches or habitat area that is occupied) as a surrogate for abundance. In cases of territorial species and where birds occur at low densities, the number of occupied patches may provide a reasonable estimate of abundance. In other cases, occupancy can be viewed as providing information about one tail of the abundance distribution, P (N = 0). The motivation for considering occupancy as a surrogate for abundance is that occupancy is based on so–called presence–absence surveys that are frequently less expensive of time and effort than methods that estimate abundance directly. We describe one set of models that can be used to estimate occupancy for a single season and another that can be used to estimate parameters such as local probabilities of extinction and colonization that are associated with occupancy dynamics. We outline a possible hybrid approach that combines occupancy data with data on marked individuals in order to betterexplore the mechanisms underlying occupancy dynamics. These five presentations made for an interesting session containing useful information and recommendations for future work. A number of themes connecting these presentations could be emphasized. For example, two of the presentations considered alternatives to standard capture–recapture sampling that can be used to draw inferences about abundance, or a portion of the abundance distribution, with field methods that should be less expensive than usual capture–recapture approaches of handling animals. We believe that the most important theme of the session was the emphasis on the processes responsible for changes in abundance. In particular, we are excited by the potential for using hierarchical models as a means of investigating relationships among vital rates and as a means of combining multiple sources of data relevant to system dynamics. Indeed, we expect the importance of this session theme to be reflected in the content and presentations of the next EURING meeting.

Animal Biodiversity and Conservation↗
USGS2010

Methylmercury cycling, bioaccumulation, and export from agricultural and non-agricultural wetlands in the Yolo Bypass

This 18-month field study addresses the seasonal and spatial patterns and processes controlling methylmercury (MeHg) production, bioaccumulation, and export from natural and agricultural wetlands of the Yolo Bypass Wildlife Area (YBWA). The data were collected in conjuntion with a Proposition 40 grant from the State Water Resources Control Board in support of the development of Best Management Practices (BMP's) for reducing MeHg loading from agricultural lands in the wetland-dominated Yolo Bypass to the Sacramento-San Joaquin River Delta. The four managemenr-based questions addressed in this study were: 1. Is there a different among agricultural and managfed wetland types in terms of Me Hg dynamic (production, degradation, bioaccumulation, or export)? 2. Does water residence time influence MeHg dynamics? 3. Does the application of sulfate-based fertilizer impact MeHg production rates? 4. Does the presence (or absence) of vegetation influence MeHg production rates? Measurements of MeHg concentrations in sediment, water, and biota (plants, invertebrates, and fish) were made to assess management-level patterns in five wetland types, which included three type of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow) and two types of managed wetlands (permanently and seasonally flooded). To strengthen our understanding of the processes underlying the seasonal and spatial patterns of MeHg cycling, additional exploratory factors were measured including ancillary sediment and water quality parameters, stable isotope fractionation (oxygen, sulfur, carbon, and nitrogen), photodemethylation rates, and daily-integrated hydrologic budgets. Samples and field data were collected from May 2007 to July 2008, and nearly all sample analyses were completed by September 2008 as per the Quality Assurance Program Plan (QAPP) requirements. Although wetland type was a major factor that drove the study design, within-field hydrology also proved to be an important factor controlling aqueous MeHg and total mercury (THg) concentrations and export. Overall, agricultural wetlands exhibited higher MeHg concentrations in overlying water, sediment, and biota than did managed seasonal and permanent wetlands. This appears to be partly due to higher rates of sediment in microbial production of MeHg on agricultural wetlands during the fall through spring period. Both sulfate- and iron-reducing bacteria have been implicated in the MeHg production process, and both were demonstrably active in all wetlands studied; however, sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands, suggesting that easily-degraded (labile) organic matter, rather than sulfate, was limiting their activity in these field types. The data suggest that agriculturally-managed soils promoted MeHg production through 1) enhanced microbial activity via higher temperatures and larger pools of labile carbon, and 2) enhanced pools of microbially available inorganic divalent mercury (Hg(II)) resulting from a decrease in reduced-sulfur, solid-phase minerals under oxic or only mildly reducing conditions. MeHg mass balances were assessed by comparing filed-specific MeHg loads for inlets vs. outlet flows. The overall mass balance for MeHg in surface water during the summer irrigation period (June - September 2007) indicated little to no net MeHg export from the six agricultural wetlands taken as a whole. Of the six agricultural wetlands, there was net overall MeHg export from two fields (one fallow and one white rice) during August, and from four of the six fields (one fallow, one white rice, and two wild rice) during September) Over the entire summer irrigation period, two of the fields (one fallow and one wild rive) showed net MeHg export, and the other four fields showed wither net import or no significant change. Rates of measured photomethylation and exchange between sediment and water pools suggest that both processes may be responsible for the lack of MeHg export. Despite significant differences during winter months between fields in surface water concentrations of MeHg, MeHg loads were not calculated in mid-winter because flood waters had overtopped field boundaries and field fidelity could not be established. During the summer 2007 irrigation season, surface water out-flows from agricultural wetlands were 9%-36% of inlet flows, and evaporation rates explained most of this water loss, with infiltration likely accounting for the remainder. Unfiltered aqueous MeHg concentrations increased from <1 ng L -1 in source waters to up to 10 ng L -1 in agricultural wetland drains during the summer irrigation period. Increases in solute concentration caused by evapoconcentration were estimated by determining concentration factors (outflow/inflow) for chloride (a conservative dissolved constituent) and by measuring oxygen isotope ratios ( 18 O/ 16 O, expressed as δ 18 O) in water. Increases in MeHg concentration from inflows-to-outflows exceeded those caused by evapoconcentration on several fields during the summer irrigation season. This was especially true when initial surface water MeHg concentrations were low, as seen in the southern block of fields receiving irrigation water directly from the Toe Drain. The northern block of fields received irrigation water from Greens Lake, which included Toe Drain water plus recirculated drain water from other agricultural fields within the Yolo Bypass and west of the Yolo Bypass; as such, the northern fields showed a smaller percentage increase in MeHg concentration because initial MeHg concentrations in surface water inflows were greater than in inputs to the southern fields. Mercury concentrations in fish were greater in agricultural wetlands white rice and wild rice) than in the two permanently flooded wetlands. Additionally, Hg concentrations in biota showed a general increase from inlets to outlets withing agricultural wetlands, but not within permanent wetlands. This was particular evident in white rice fields where caged western mosquitofish at the outlets had Hg concentrations that were more than 4 times higher than in caged fish held at the inlets. Similar spatial patterns in Hg bioaccumulation in agricultural and permanent wetlands were seen for wild populations of western mosquitofish and Mississippi silversides. In contrast to fish, invertebrates, such as water-boatman (Corixidae) and back swimmers (Notonectidae), had greater Hg concentrations in permanent wetlands than in tempoarirly flooded agricultural wetlands, Fish THg concentrations were weakly correlated with water MeHg,a and not correlated with sediment MeHg. In contrast, invertebrate MeHg concentrations were more strongly correlated with sediment MeHg than with water MeHg concentrations. These results illustrate the complexity of MeHg bioaccumulation through food webs and indicate the importance of simultaneously using multiple biosentinels when monitoring MeHg production and bioaccumulation. Despite high sediment production rates and water concentrations in agricultural wetlands, MeHg export was physically limited by hydrologic export for all wetlands studied. We suggest that load reduction is maximized by limiting water throughout, but that on-site biota exposure is maximized by this loner water residence time. While field-specific hydrologic loads could not be fully quantified during flood conditions in February 2008, we suggest that the primary period of MeHg export from Yolo Bypass Wildlife Area is during those winter flooding periods when overall microbial activity and MeHg production in agricultural soils is fueled by the decomposition of rice straw, and when hydrologic flowthrough is maximal. Local stakeholders participated in two workshops related to this study, demonstrating an interest in understanding factors controlling MeHg production, export, and bioaccumulation. The results of this field study show that permanently flooded, naturally vegetated wetlands are unlikely to a large source of MeHg production within the YBWA, in contrast with agriculturally-managed wetlands. MeHg loading to Toe Drain waters of the Yolo Bypass may be reduced by lowering rated of hydrologic export from agricultural wetlands during the growing season and especially during rice harvest, However, under these water-holding conditions, biota living within agricultural wetlands may thus be exposed to higher MeHg concentrations in surface water, As observed in this study, rapid bioacculumaltion over a 2-month period led to MeHg concentrations in invertebrates and fish more than 6 and 11 times higher, respectively, than proposed TMDL target values to protect wildlife (0.03 ppm ww). The results of this field study, together with the information from YBWA stakeholders, provide a more definitive understanding of how MeHg cycling and bioaccumulation respond to habitat differences and specific management practices. These results directly address 4 core components of CBDA's Mercury Strategy for the Bay-Delta Ecosystem (Wiener et al., 2003a): a) Quantification and evaluation of THg and MeHg sources, b) Quantification of effects of ecosystem restoration on MeHg exposure, c) Assessment of ecological risk, and d) Identification and testing of potential management approaches for reducing MeHg contamination. In addition, the quantitative results reported here assess the effect of current land use practices in the Yolo Bypass MeHg production, bioaccumulation and export, and provide process-based advice towards achieving current goals of the RWQCB-CVR's Sacramento -- San Joaquin Delta Estuary TMDL for Methyl & Total Mercury (Wood et al., 2010b). Further work is necessary to evaluate biotic exposure in the Yolo Bypass Wildlife Area at higher trophic levels (e.g. birds), to quantify winter hydrologic flux of MeHg to the larger Delta ecosystem, and to evaluate rice straw management options to limit labile carbon supplies to surface sediment during winter months. In summary, agricultural management of rice fields -- specifically the periodic flooding and production of easily degraded organic matter -- promotes the production of MeHg beyond rates seen in naturally vegetated wetlands, whether seasonally or permanently flooded., The exported load from MeHg from these agricultural wetlands may be controlled by limiting hydrologic export from fields to enhance on-site MeHg removal processes, but the tradeoff is that this impoundement increases Me Hg exposure to resident organisms.

California↗
USGS1996

Manufacture of ammonium sulfate fertilizer from gypsum-rich byproduct of flue gas desulfurization - A prefeasibility cost estimate

Costs for constructing and operating a conceptual plant based on a proposed process that converts flue gas desulfurization (FGD)-gypsum to ammonium sulfate fertilizer has been calculated and used to estimate a market price for the product. The average market price of granular ammonium sulfate ($138/ton) exceeds the rough estimated cost of ammonium sulfate from the proposed process ($111/ ton), by 25 percent, if granular size ammonium sulfate crystals of 1.2 to 3.3 millimeters in diameters can be produced by the proposed process. However, there was at least ??30% margin in the cost estimate calculations. The additional costs for compaction, if needed to create granules of the required size, would make the process uneconomical unless considerable efficiency gains are achieved to balance the additional costs. This study suggests the need both to refine the crystallization process and to find potential markets for the calcium carbonate produced by the process.

ACS Division of Fuel Chemistry, Preprints↗
USGS1999

Protocol and practice in the adaptive management of waterfowl harvests

Waterfowl harvest management in North America, for all its success, historically has had several shortcomings, including a lack of well-defined objectives, a failure to account for uncertain management outcomes, and inefficient use of harvest regulations to understand the effects of management. To address these and other concerns, the U.S. Fish and Wildlife Service began implementation of adaptive harvest management in 1995. Harvest policies are now developed using a Markov decision process in which there is an explicit accounting for uncontrolled environmental variation, partial controllability of harvest, and structural uncertainty in waterfowl population dynamics. Current policies are passively adaptive, in the sense that any reduction in structural uncertainty is an unplanned by-product of the regulatory process. A generalization of the Markov decision process permits the calculation of optimal actively adaptive policies, but it is not yet clear how state-specific harvest actions differ between passive and active approaches. The Markov decision process also provides managers the ability to explore optimal levels of aggregation or "management scale" for regulating harvests in a system that exhibits high temporal, spatial, and organizational variability. Progress in institutionalizing adaptive harvest management has been remarkable, but some managers still perceive the process as a panacea, while failing to appreciate the challenges presented by this more explicit and methodical approach to harvest regulation. Technical hurdles include the need to develop better linkages between population processes and the dynamics of landscapes, and to model the dynamics of structural uncertainty in a more comprehensive fashion. From an institutional perspective, agreement on how to value and allocate harvests continues to be elusive, and there is some evidence that waterfowl managers have overestimated the importance of achievement-oriented factors in setting hunting regulations. Indeed, it is these unresolved value judgements, and the lack of an effective structure for organizing debate, that present the greatest threat to adaptive harvest management as a viable means for coping with management uncertainty. Copyright ?? 1999 by The Resilience Alliance.

Conservation Ecology↗
USGS2015

Automated extraction of natural drainage density patterns for the conterminous United States through high performance computing

Hydrographic networks form an important data foundation for cartographic base mapping and for hydrologic analysis. Drainage density patterns for these networks can be derived to characterize local landscape, bedrock and climate conditions, and further inform hydrologic and geomorphological analysis by indicating areas where too few headwater channels have been extracted. But natural drainage density patterns are not consistently available in existing hydrographic data for the United States because compilation and capture criteria historically varied, along with climate, during the period of data collection over the various terrain types throughout the country. This paper demonstrates an automated workflow that is being tested in a high-performance computing environment by the U.S. Geological Survey (USGS) to map natural drainage density patterns at the 1:24,000-scale (24K) for the conterminous United States. Hydrographic network drainage patterns may be extracted from elevation data to guide corrections for existing hydrographic network data. The paper describes three stages in this workflow including data pre-processing, natural channel extraction, and generation of drainage density patterns from extracted channels. The workflow is concurrently implemented by executing procedures on multiple subbasin watersheds within the U.S. National Hydrography Dataset (NHD). Pre-processing defines parameters that are needed for the extraction process. Extraction proceeds in standard fashion: filling sinks, developing flow direction and weighted flow accumulation rasters. Drainage channels with assigned Strahler stream order are extracted within a subbasin and simplified. Drainage density patterns are then estimated with 100-meter resolution and subsequently smoothed with a low-pass filter. The extraction process is found to be of better quality in higher slope terrains. Concurrent processing through the high performance computing environment is shown to facilitate and refine the choice of drainage density extraction parameters and more readily improve extraction procedures than conventional processing.

Conference Paper↗
USGS2014

Two approaches for incorporating climate change into natural resource management planning at Wind Cave National Park

Wind Cave National Park (WICA) protects one of the world’s longest caves, has large amounts of high quality, native vegetation, and hosts a genetically important bison herd. The park’s relatively small size and unique purpose within its landscape requires hands-on management of these and other natural resources, all of which are interconnected. Anthropogenic climate change presents an added challenge to WICA natural resource management because it is characterized by large uncertainties, many of which are beyond the control of park and National Park Service (NPS) staff. When uncertainty is high and control of this uncertainty low, scenario planning is an appropriate tool for determining future actions. In 2009, members of the NPS obtained formal training in the use of scenario planning in order to evaluate it as a tool for incorporating climate change into NPS natural resource management planning. WICA served as one of two case studies used in this training exercise. Although participants in the training exercise agreed that the scenario planning process showed promise for its intended purpose, they were concerned that the process lacked the scientific rigor necessary to defend the management implications derived from it in the face of public scrutiny. This report addresses this concern and others by (1) providing a thorough description of the process of the 2009 scenario planning exercise, as well as its results and management implications for WICA; (2) presenting the results of a follow-up, scientific study that quantitatively simulated responses of WICA’s hydrological and ecological systems to specific climate projections; (3) placing these climate projections and the general climate scenarios used in the scenario planning exercise in the broader context of available climate projections; and (4) comparing the natural resource management implications derived from the two approaches. Wind Cave National Park (WICA) protects one of the world’s longest caves, has large amounts of high quality, native vegetation, and hosts a genetically important bison herd. The park’s relatively small size and unique purpose within its landscape requires hands-on management of these and other natural resources, all of which are interconnected. Anthropogenic climate change presents an added challenge to WICA natural resource management because it is characterized by large uncertainties, many of which are beyond the control of park and National Park Service (NPS) staff. When uncertainty is high and control of this uncertainty low, scenario planning is an appropriate tool for determining future actions. In 2009, members of the NPS obtained formal training in the use of scenario planning in order to evaluate it as a tool for incorporating climate change into NPS natural resource management planning. WICA served as one of two case studies used in this training exercise. Although participants in the training exercise agreed that the scenario planning process showed promise for its intended purpose, they were concerned that the process lacked the scientific rigor necessary to defend the management implications derived from it in the face of public scrutiny. This report addresses this concern and others by (1) providing a thorough description of the process of the 2009 scenario planning exercise, as well as its results and management implications for WICA; (2) presenting the results of a follow-up, scientific study that quantitatively simulated responses of WICA’s hydrological and ecological systems to specific climate projections; (3) placing these climate projections and the general climate scenarios used in the scenario planning exercise in the broader context of available climate projections; and (4) comparing the natural resource management implications derived from the two approaches.

Report↗
USGS2009

Adaptive management: The U.S. Department of the Interior technical guide

The purpose of this technical guide is to present an operational definition of adaptive management, identify the conditions in which adaptive management should be considered, and describe the process of using adaptive management for managing natural resources. The guide is not an exhaustive discussion of adaptive management, nor does it include detailed specifications for individual projects. However, it should aid U.S. Department of the Interior (DOI) managers and practitioners in determining when and how to apply adaptive management. Adaptive management is framed within the context of structured decision making, with an emphasis on uncertainty about resource responses to management actions and the value of reducing that uncertainty to improve management. Though learning plays a key role in adaptive management, it is seen here as a means to an end, namely good management, and not an end in itself. The operational definition used in the guide is adopted from the National Research Council, which characterizes adaptive management as an iterative learning process producing improved understanding and improved management over time: Adaptive management [is a decision process that] promotes flexible decision making that can be adjusted in the face of uncertainties as outcomes from management actions and other events become better understood. Careful monitoring of these outcomes both advances scientific understanding and helps adjust policies or operations as part of an iterative learning process. Adaptive management also recognizes the importance of natural variability in contributing to ecological resilience and productivity. It is not a ‘trial and error’ process, but rather emphasizes learning while doing. Adaptive management does not represent an end in itself, but rather a means to more effective decisions and enhanced benefits. Its true measure is in how well it helps meet environmental, social, and economic goals, increases scientific knowledge, and reduces tensions among stakeholders. Adaptive management as defined here involves ongoing, real-time learning and knowledge creation, both in a substantive sense and in terms of the adaptive process itself. It is described in what follows in a series of 9 steps, as summarized in section 4.1, involving stakeholder involvement, management objectives, management alternatives, predictive models, monitoring plans, decision making, monitoring responses to management, assessment, and adjustment to management actions. An adaptive approach actively engages stakeholders in all phases of a project over its timeframe, facilitating mutual learning and reinforcing the commitment to learning-based management. Adaptive management in DOI is implemented within a legal context that includes statutory authorities such as the National Environmental Policy Act (NEPA), the Endangered Species Act, and the Federal Advisory Committee Act. For many important problems now facing the resource management community, adaptive management holds great promise in reducing the uncertainties that limit the effective management of natural resource systems. For many conservation and management problems, utilizing management itself in an experimental context may be the only feasible way to gain the system understanding needed to improve management. Though it is commonly thought that an adaptive approach can produce results quickly at low cost, the opposite is more likely to be true. An initial investment of time and effort will increase the likelihood of better decision making and resource stewardship in the future, but patience, flexibility, and support are needed over the life of an adaptive management project. For these reasons it is important to carefully consider the potential use of an adaptive approach, and to engage in careful planning and evaluation when adaptive management is used.

Report↗
USGS1996

Small watershed studies: Analytical approaches for understanding ecosystem response to environmental change

Biogeochemical studies in small watersheds provide an analytical approach to understand how ecosystems respond to natural climatic variations and human-induced environmental change. Small watersheds, usually less than 5 km2, are small enough to permit characterization and understanding of ecosystem processes within relatively simple, homogeneous biological and physical settings; yet they are large enough to incorporate more complex processes and element cycles than can be studied at plot scales. Watersheds comprise discrete hydrochemical environments allowing quantification of hydrologic, element, and energy budgets. Element budgets, or mass balances, can be quantified as the difference between the mass of a solute that enters a watershed in wet and dry deposition and leaves a watershed in streamflow. Element budgets are primary tools used to investigate biogeochemical processes. Monitoring various aspects of element budgets to assess ecosystem health and stability is analogous to measuring the pulse or blood chemistry of a patient. Monitoring streamwater chemistry, basic climate, soil, and biotic variables provide a means to integrate complex biogeochemical processes and evaluate trends in water quality. Small watershed studies provide a scientific basis to develop predictive models of watershed function. Major emphases of small watershed studies include investigation of hydrologic and chemical responses to natural climate variation, anthropogenic stressors, and alternate forest-management practices. The nature and significance of biogeochemical research in small watersheds is reviewed by Moldan and Cerny (1994). The U.S. Geological Survey, U.S. Department of Agriculture Forest Service, and other federal agencies support several long-term small watershed studies to provide insight into a variety of ecosystem processes. Long-term records are essential to distinguish trends resulting from natural climatic variations or other stressors. The following sites, with noted periods of records, are examples of intensively studied forested watersheds in eastern USA supported by federal agencies: ■ Coweeta Hydrologic Laboratory, North Carolina, (1939-present), Swank and Crossley (1988). ■ Hubbard Brook Experimental Forest, New Hampshire, (1956-present), Bormann and Likens (1979). ■ Sleepers River Research Watershed, Vermont, (1958-present), Shanley et al. (1995). ■ Walker Branch Watershed, Tennessee, (1967-present), Johnson and Van Hook (1989). ■ Catoctin Mountains Research Site, Maryland, (1982-present), Rice and Bricker (1995). ■ Catskill Stream Network, New York, (1983- present), Murdoch and Stoddard (1992). ■ Panola Mountain Research Watershed, Georgia, (1985-present), Huntington et al. (1993). Small watershed studies also provide essential baseline information for understanding variations in water quality and element cycling in "pristine" ecosystems that can be used as benchmarks to evaluate anthropogenic impacts and alternate watershed management practices. This paper provides examples of how analytical tools developed through watershed research provide insight into ecosystem processes and can contribute to the management of watershed resources.

Conference Paper↗
USGS1981

Geology and concepts of genesis of important types of uranium deposits

Uranium ore deposits occur in nearly every major rock type in the earth’s crust, and nearly all igneous, metamorphic, and sedimentary processes are capable of concentrating or dispersing uranium. However, only three types of deposits account for more than 70 percent of known Western World Reasonably Assured Resources (WWRAR): Precambrian quartz-pebble conglomerate type, Proterozoic unconformity type, and Phanerozoic sandstone type. Igneous-related processes in plutonic, volcanic, and magmatic-hydrothermal environments, considered important 25 years ago, now account for less than 10 percent of world resources known at present. The oldest known ore deposits were formed in conglomerates by placer processes under unique anoxic conditions. For the last 2.2 b.y., since oxygenation of the atmosphere, the genesis of both high- and low-temperature deposits has been dominated by three general geochemical processes: (1) oxidation of uranium to soluble U(VI) species permitting aqueous transport, perhaps most commonly as uranyl-carbonate complexes; (2) reduction, principally by C, S −2 , or Fe +2 species, to U(IV) to allow precipitation of uraninite (pitchblende), and coffinite, although the specific reductant commonly cannot be determined because these three tend to be associated geologically; and (3) igneous and metamorphic differentiation caused by exclusion of uranium from crystal structure of most rock-forming minerals. The geochemistry of uranium ore-forming processes has changed in time because of the evolution of life forms and their impact on the earth’s oxygen and carbon budgets. This evolution is reflected in changing predominance of ore types in geologic time: (1) pre-2.8 b.y. ago—no known uranium ore deposits; (2) ca. 2.8 to 2.2 b.y. ago—the first intràcratonic basins and anoxic atmosphere permitted accumulation of placer deposits of uraninite in quartz-pebble conglomerates; these deposits contain about 19 percent of the western world’s resources; (3) ca. 2.2 to 0.4 b.y. ago—following oxygenation of the atmosphere uranium was oxidized and transported as soluble U(VI) complexes to sites of reduction, commonly in organic carbon-rich marginal marine environments. Diagenesis, metamorphism, and near-surface redox enrichment subsequently formed unconformity-type, ultrametamorphic-type, and vein-type ore deposits which together contain more than 25 percent of the western world’s resources; (4) ca. 0.4 b.y. ago to present—after development of land plants the most important ore-forming process was redox-controlled deposition from ground water in continental sediments. Sandstone-type deposits, characteristic of this stage, contain about 40 percent of the western world’s resources.

Book chapter↗
USGS2021

Toward improved decision-support tools for Delta Smelt management actions

The Collaborative Science and Adaptive Management Program (CSAMP) has endorsed a goal of reversing the recent downward trajectory of the Delta Smelt population within 5-10 generations, with the long-term aim of establishing a self-sustaining population. An ambitious agenda of management actions is planned, and more management actions are being considered. This White Paper furthers one of the recommendations in the 2019 Delta Smelt Science Plan – the need to predict the potential ecological effects of taking a management action. Existing statistical models can be highly informative in assessing the response of Delta Smelt to changing system conditions and management actions. However, management actions can shift or alter conditions in ways that models based on analysis of historical data may not be able to represent, and short-term or localized effects may be missed with models designed to assess effects at the population level. Decision support tools (DSTs) are computer-based tools developed to assist decision-making, often combining computationally intensive analysis and spatial mapping of environmental relationships. DSTs can be used in planning processes that evaluate an array of actions, such as in Structured Decision Making (SDM), where DSTs are needed to compare among alternatives. DSTs can also be used to explore the potential effects of different approaches to implementing management actions. The goal of this White Paper is to identify plausible options for DSTs that could be developed for future use to evaluate management actions that seek to either reverse the decline of Delta Smelt or minimize or mitigate the effects of other water management actions. Different types of management actions lead to different needs for DSTs. This White Paper was developed using three types of actions currently being considered to enhance the Delta Smelt population: Supplementation with Hatchery Fish, Summer-Fall Habitat, and Food Enhancement actions. These three management actions target different parts of the estuary and different processes, with a variety of possible metrics to gauge performance. Three DSTs are proposed that collectively address management questions related to the management actions considered, with each requiring a slightly different set of processes to be included and producing an array of outputs at varying spatial and temporal scales: DST 1. Modeling Fish Movement, Survival, and Reproduction Across Their Range. This DST can address management questions that require information about Delta Smelt spatial distribution and movement. • DST 1 could be used to compare conditions with and without management actions in place, how the management action performs among different types of water years (with varied flow and associated abiotic conditions), and to assess relative change with different variations and strategies of the management actions. • DST 2. Changes in Habitat Conditions and Delta Smelt Response. This DST is intended to evaluate combinations of conditions that are considered to provide suitable habitat for Delta Smelt, and Delta Smelt response. Delta Smelt habitat is generally described as open water with low salinity (0 to 6), turbidity of at least 12 NTU, suitable temperature conditions, and sufficient food availability to support growth. • DST 3. Regional Effects of Food Subsidy. This DSTs seeks to evaluate effectiveness of food enhancement actions by providing information on responses of the immediate targets of the action (i.e., phytoplankton or zooplankton) and tracing those to projected growth responses of Delta Smelt. There is not a single DST that adequately addresses management questions relevant to all management actions, although there is some overlap in the management questions each of the three DSTs can address. For each of the DSTs a substantial foundation of models and approaches already exists and modeling has already been applied to several of the management actions described. However, a number of outstanding issues remain for further development of the proposed DSTs. These are summarized in this White Paper together with potential approaches that could be applied or tested. Some components for the DSTs are already available and thus development could be relatively easy. However, for several of the topics identified there are gaps in knowledge that currently limit formulation of model structure and process representations. This presents challenges to readily incorporate some needed mechanisms into the models. Eleven next steps, aligned with relevant DSTs, are outlined. The next steps vary in their complexity or technical ‘lift’ required. Many build on existing work, or methods and approaches that have already been developed or are underway, while others require additional thinking to establish a viable approach. Some interim utility for decisions could be gained during initial development of the DSTs with further features added over time. Development of a DST requires engagement of both managers and scientists. Identifying the outputs and resolution needed for management purposes early in development of any DST is essential for effective pursuit of next steps and suitable approaches to address challenges. Dialog between managers and technical experts also informs what process-based simulation can do, and what tradeoffs are acceptable to meet a given purpose. To further develop the DSTs outlined here for application in the estuary requires: - Engagement of a committed group of technical experts with appropriate expertise. - The development of a coordinated workplan including appropriate project management and tracking. - Dialog between potential users (i.e., managers and policy makers) and technical experts. - Resources to pursue DST development including personnel and computational resources. This White Paper demonstrates the potential for moving toward DSTs for a variety of management actions in support of Delta Smelt that include mechanistic representations of physical and biological processes. Through focused effort from technical experts, managers and policy makers, DSTs can be developed to provide quantitative predictions of management effects on the ecosystem, targeting the changes the management actions seek to achieve, how these effects compare to ambient conditions, and how the effects vary among water year types or with timing and location of actions. Importantly, solid foundations exist which can be leveraged, refined, and built upon to specifically inform current and future management decisions.

White Paper↗
USGS2022

Section 5: Remote sensing of vegetation in the riparian corridor of the Colorado River’s delta 2013-2018

This remote sensing section is based on Nagler et al. (in preparation for the journal Hydrological Processes) and is a summary of the USGS preliminary findings to date. This report documents the changes in green foliage density (greenness) as measured by satellite vegetation index (VI) data and corresponding evapotranspiration (ET) in the riparian corridor of the Colorado River delta associated with the Minutes 319 and 323 environmental water deliveries using time-series data from 2013 through 2018. The report focuses on what happened only within the riparian corridor’s seven reaches since the 2014 flows, and despite being a continuation of measuring greenness and ET after the 2017 end of Minute 319, this study continued the tracking of these two variables, greenness and ET, in these original riparian corridor focal areas. Two spatial scales are used here: (1) Landsat satellite imagery at 30 m pixels and (2) the EOS-1 satellite sensor the Moderate Resolution Imaging Spectrometer (MODIS) with a resolution of 250 m pixels. The focal period includes 2013 (prepulse flow) and the years 2014-2018, with a focus on imagery collected from the Summer growing seasons 2014 through 2018 (one-year, pre-pulse and several post-pulse years, respectively). This report re-creates the 2013-2017 Landsat-based results from Jarchow et al. (2017a, b) by using the same region of interest (ROI). The report now provides revised and re-created results using all new imagery acquisition and processing techniques, as well as extraction code, created by the Vegetation Index and Phenology (VIP) Lab of the Biosystems Engineering Department of the University of Arizona (UofA). In 2018, methods employed by the VIP lab (and not ArcGIS) were used. ArcGIS was only used in the newly processed data to display the final difference maps. The entire spatial tile data from NASA was downloaded and processed at the VIP Lab using satellite imagery at two resolutions: 250 m MODIS and 30 m Landsat using three sensors, Landsat 5, Landsat 7 ETM+ and Landsat 8 Operational Land Imager (OLI), with added scenes for each year based on new clear atmosphere requirements. The VIP lab clipped the river boundary and seven riparian reaches from the previously existing ROI used in Jarchow et al. (2017 a, b) for the analyses done under Minute 319. The NASA image datasets for this riparian corridor ROI in seven reaches were re-processed to produce additional vegetation index (VI) information for years 2013 to 2018 for this report. At the same time, the report acquired and processed imagery from 2000- 2018 (data outside the scope of this report and data not shown here). The additional VIs (NDVI, scaled NDVI, EVI, EVI2) were analyzed so that new assessments of greenness and ET could be produced from the imagery datasets following methods in Nagler et al. (2013). These VI choices were based on previous performance comparisons between biophysical ground-based data and radiometric satellite-based data collected from this riparian ecosystem (Nagler et al., 2001) as well as performance related to ET estimation (Nagler et al., 2005a, b) and current advancements in VIs such as EVI2.

Colorado River Delta↗
USGS2016

The role of crystallization-driven exsolution on the sulfur mass balance in volcanic arc magmas

The release of large amounts of sulfur to the stratosphere during explosive eruptions affects the radiative balance in the atmosphere and consequentially impacts climate for up to several years after the event. Quantitative estimations of the processes that control the mass balance of sulfur between melt, crystals, and vapor bubbles is needed to better understand the potential sulfur yield of individual eruption events and the conditions that favor large sulfur outputs to the atmosphere. The processes that control sulfur partitioning in magmas are (1) exsolution of volatiles (dominantly H 2 O) during decompression (first boiling) and during isobaric crystallization (second boiling), (2) the crystallization and breakdown of sulfide or sulfate phases in the magma, and (3) the transport of sulfur-rich vapor (gas influx) from deeper unerupted regions of the magma reservoir. Vapor exsolution and the formation/breakdown of sulfur-rich phases can all be considered as closed-system processes where mass balance arguments are generally easier to constrain, whereas the contribution of sulfur by vapor transport (open system process) is more difficult to quantify. The ubiquitous “excess sulfur” problem, which refers to the much higher sulfur mass released during eruptions than what can be accounted for by amount of sulfur originally dissolved in erupted melt, as estimated from melt inclusion sulfur concentrations (the “petrologic estimate”), reflects the challenges in closing the sulfur mass balance between crystals, melt, and vapor before and during a volcanic eruption. In this work, we try to quantify the relative importance of closed- and open-system processes for silicic arc volcanoes using kinetic models of sulfur partitioning during exsolution. Our calculations show that crystallization-induced exsolution (second boiling) can generate a significant fraction of the excess sulfur observed in crystal-rich arc magmas. This result does not negate the important role of vapor migration in sulfur mass balance but rather points out that second boiling (in situ exsolution) can provide the necessary yield to drive the excess sulfur to the levels observed for crystal-rich systems. In contrast, in crystal-poor systems, magma recharge that releases sulfur-rich bubbles is necessary and most likely the primary contributor to sulfur mass balance. Finally, we apply our model to account for the effect of sulfur partitioning during second boiling and its impact on sulfur released during the Cerro Galan supereruption in Argentina (2.08 Ma) and show the potential importance of second boiling in releasing a large amount of sulfur to the atmosphere during the eruption of large crystal-rich ignimbrites.

Journal of Geophysical Research B: Solid Earth↗
USGS2021

An integrated path for spatial capture–recapture and animal movement modeling

Ecologists and conservation biologists increasingly rely on spatial capture–recapture (SCR) and movement modeling to study animal populations. Historically, SCR has focused on population-level processes (e.g., vital rates, abundance, density, and distribution), whereas animal movement modeling has focused on the behavior of individuals (e.g., activity budgets, resource selection, migration). Even though animal movement is clearly a driver of population-level patterns and dynamics, technical and conceptual developments to date have not forged a firm link between the two fields. Instead, movement modeling has typically focused on the individual level without providing a coherent scaling from individual- to population-level processes, whereas SCR has typically focused on the population level while greatly simplifying the movement processes that give rise to the observations underlying these models. In our view, the integration of SCR and animal movement modeling has tremendous potential for allowing ecologists to scale up from individuals to populations and advancing the types of inferences that can be made at the intersection of population, movement, and landscape ecology. Properly accounting for complex animal movement processes can also potentially reduce bias in estimators of population-level parameters, thereby improving inferences that are critical for species conservation and management. This introductory article to the Special Feature reviews recent advances in SCR and animal movement modeling, establishes a common notation, highlights potential advantages of linking individual-level (Lagrangian) movements to population-level (Eulerian) processes, and outlines a general conceptual framework for the integration of movement and SCR models. We then identify important avenues for future research, including key challenges and potential pitfalls in the developments and applications that lie ahead.

Ecology↗
USGS2022

Evaluating hydrologic region assignment techniques for ungaged basins in Alaska, USA

Building continental-scale hydrologic models in data-sparse regions requires an understanding of spatial variation in hydrologic processes. Extending these models to ungaged locations requires techniques to group ungaged locations with gaged ones to make process importance and model parameter transfer decisions to ungaged locations. This analysis (1) tested the utility of fundamental streamflow statistics (FDSS) in defining hydrologic regions across Alaska, USA; (2) evaluated if the hydrologic regions represented different hydrologic processes; and (3) tested the ability of random forest and direct assignment techniques, informed by statistically estimated FDSS (FDSSest) and basin characteristics (BCs), to correctly assign ungaged locations to hydrologic regions. Six hydrologic regions were identified across the domain using FDSS. Differences in mean flow, phase shift of the seasonal cycle, and skewness were the primary characteristics defining each region. Two regions represented arctic and continental climates, generally in the northern portion of the domain; four regions represented the southern, maritime portion of the domain. Random forest modeling with BCs (67% success rate) outperformed FDSSest (58% success rate) suggesting that no statistically estimated streamflow was needed to assign ungaged locations to a region. For regions with many sites, most region assignment techniques performed similarly. Random forest modeling performance declined when BCs and FDSSest were both used to predict region membership, suggesting FDSSest had little information in addition to BCs. This analysis demonstrated that FDSS-based hydrologic regions discern process differences across a data-sparse and hydrologically diverse landscape. Process importance rankings from random forest-derived BCs provided model-independent information for making modeling decisions.

Alaska↗
USGS2006

Rime and graupel: Description and characterization as revealed by low-temperature scanning electron microscopy

Snow crystals, which form by vapor deposition, occasionally come in contact with supercooled cloud droplets during their formation and descent. When this occurs, the droplets adhere and freeze to the snow crystals in a process known as accretion. During the early stages of accretion, discrete snow crystals exhibiting frozen cloud droplets are referred to as rime. If this process continues, the snow crystal may become completely engulfed in frozen cloud droplets. The resulting particle is known as graupel. Light microscopic investigations have studied rime and graupel for nearly 100 years. However, the limiting resolution and depth of field associated with the light microscope have prevented detailed descriptions of the microscopic cloud droplets and the three-dimensional topography of the rime and graupel particles. This study uses low-temperature scanning electron microscopy to characterize the frozen precipitates that are commonly known as rime and graupel. Rime, consisting of frozen cloud droplets, is observed on all types of snow crystals including needles, columns, plates, and dendrites. The droplets, which vary in size from 10 to 100 &mu;m, frequently accumulate along one face of a single snow crystal, but are found more randomly distributed on aggregations consisting of two or more snow crystals (snowflakes). The early stages of riming are characterized by the presence of frozen cloud droplets that appear as a layer of flattened hemispheres on the surface of the snow crystal. As this process continues, the cloud droplets appear more sinuous and elongate as they contact and freeze to the rimed crystals. The advanced stages of this process result in graupel, a particle 1 to 3 mm across, composed of hundreds of frozen cloud droplets interspersed with considerable air spaces; the original snow crystal is no longer discernible. This study increases our knowledge about the process and characteristics of riming and suggests that the initial appearance of the flattened hemispheres may result from impact of the leading face of the snow crystal with cloud droplets. The elongated and sinuous configurations of frozen cloud droplets that are encountered on the more advanced stages suggest that aerodynamic forces propel cloud droplets to the trailing face of the descending crystal where they make contact and freeze.

Scanning↗
USGS2015

Application of science-based restoration planning to a desert river system

Persistence of many desert river species is threatened by a suite of impacts linked to water infrastructure projects that provide human water security where water is scarce. Many desert rivers have undergone regime shifts from spatially and temporally dynamic ecosystems to more stable systems dominated by homogenous physical habitat. Restoration of desert river systems could aid in biodiversity conservation, but poses formidable challenges due to multiple threats and the infeasibility of recovery to pre-development conditions. The challenges faced in restoring desert rivers can be addressed by incorporating scientific recommendations into restoration planning efforts at multiple stages, as demonstrated here through an example restoration project. In particular, use of a watershed-scale planning process can identify data gaps and irreversible constraints, which aid in developing achievable restoration goals and objectives. Site-prioritization focuses limited the resources for restoration on areas with the greatest potential to improve populations of target organisms. Investment in research to understand causes of degradation, coupled with adoption of a guiding vision is critical for identifying feasible restoration actions that can enhance river processes. Setting monitoring as a project goal, developing hypotheses for expected outcomes, and implementing restoration as an experimental design will facilitate adaptive management and learning from project implementation. Involvement of scientists and managers during all planning stages is critical for developing process-based restoration actions and an implementation plan to maximize learning. The planning process developed here provides a roadmap for use of scientific recommendations in future efforts to recover dynamic processes in imperiled riverine ecosystems.

San Rafael River watershed↗
USGS2023

Becoming an actionable scientist: Challenges, competency, and the development of expertise

Demand has grown for actionable science to support real-world decision-making around climate change and related environmental management challenges. Producing actionable science requires scientists to hold a distinct set of competencies, yet relatively little is known about what these competencies are or how to train scientists to develop them. We conducted interviews with mid- and late-career scientists to empirically identify competencies they used when producing actionable science and to understand how they developed those competencies. We describe expertise in terms of 18 competencies—categorised as cognitive, interpersonal, or intrapersonal—that scientists integrated and applied to address the challenges associated with actionable science. We argue that scientists must engage in the social process of producing actionable science (i.e., learning by doing) to become an expert. Expert actionable scientists discussed the importance of learning through different contexts, processes, interactions, and relationships. By naming the competencies that constitute expertise, as well as methods for expertise development, our findings facilitate greater conscious awareness of the process of becoming an actionable scientist, a gradual process that starts during graduate training and continues as a career proceeds. Our results can inform the development of formal learning opportunities as well as the informal learning process that occurs whereby scientists take charge of their own learning.

Environmental Management↗
USGS2005

Geochemistry and the understanding of ground-water systems

Geochemistry has contributed significantly to the understanding of ground-water systems over the last 50 years. Historic advances include development of the hydrochemical facies concept, application of equilibrium theory, investigation of redox processes, and radiocarbon dating. Other hydrochemical concepts, tools, and techniques have helped elucidate mechanisms of flow and transport in ground-water systems, and have helped unlock an archive of paleoenvironmental information. Hydrochemical and isotopic information can be used to interpret the origin and mode of ground-water recharge, refine estimates of time scales of recharge and ground-water flow, decipher reactive processes, provide paleohydrological information, and calibrate ground-water flow models. Progress needs to be made in obtaining representative samples. Improvements are needed in the interpretation of the information obtained, and in the construction and interpretation of numerical models utilizing hydrochemical data. The best approach will ensure an optimized iterative process between field data collection and analysis, interpretation, and the application of forward, inverse, and statistical modeling tools. Advances are anticipated from microbiological investigations, the characterization of natural organics, isotopic fingerprinting, applications of dissolved gas measurements, and the fields of reaction kinetics and coupled processes. A thermodynamic perspective is offered that could facilitate the comparison and understanding of the multiple physical, chemical, and biological processes affecting ground-water systems.

Hydrogeology Journal↗