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USGS2024

State of the data: Assessing the FAIRness of USGS data

In response to recent shifts towards open science that emphasize transparency, reproducibility, and access to research data, the US Geological Survey (USGS) conducted a study to assess the degree to which USGS data assets meet the FAIR data principles (Findable, Accessible, Interoperable, and Reusable). The USGS designed and applied a methodology for quantitative analysis of FAIR characteristics. A new rubric was derived from a crosswalk of existing FAIR evaluation frameworks and customized for the USGS. The rubric, consisting of 62 yes/no questions, was applied to 392 metadata records of USGS data products published between 1987 and 2022. Results were analyzed to show which FAIR characteristics were most and least present in the metadata and how these scores changed after the implementation of data policy requirements in 2016. Aggregated scores showed specific areas of strength and needed improvements. The greatest increases in FAIR scores over time were for elements that were required by new data policies, especially in the ‘Findable’ category. Based on the results, this paper presents strategies to further improve USGS alignment with FAIR. The suggested strategies are organized in four key areas: USGS data repository characteristics, training and communities of practice, data management policy considerations, and metadata standards, tools, and best practices.

Data Science Journal↗

USGS2020

Comparing environmental flow implementation options with structured decision making: Case study from the Willamette River, Oregon

Many frameworks have been used to identify environmental flows for sustaining river ecosystems or specific taxa in the face of widespread flow alteration for human use. However, these methods mostly focus on identifying suitable flows and largely ignore the important links between management actions, resulting flows, flow variability, and ecosystem or social responses. Structured decision making (SDM) could assist the comparison and implementation of environmental flows by providing a framework to compare effects of flow management actions on objectives via environmental flow science. We describe the SDM process and illustrate its application using a case study focused on comparing environmental flow scenarios for the mainstem Willamette River, Oregon, USA. In a short timeframe, SDM was successfully applied to identify management objectives, develop empirical and expert opinion based models predicting ecological responses, and compare scenarios while accounting for uncertainty and partial controllability. We found that no flow scenario was clearly preferred based on available knowledge, largely because river flows could only be partially controlled through available dam operations. Participants agreed that the SDM process was useful and that an additional iteration focused on refining predictive models and incorporating additional objectives could help better inform dam release decisions for the entire basin. In our view, SDM can provide managers with more realistic comparisons of environmental flows by accounting for partial controllability and uncertainty, which may result in greater implementation of available flow management actions.

Oregon↗

USGS2020

Decision analysis for greater insights into the development and evaluation of Chinook salmon restoration strategies in California’s Central Valley

Considerable amounts of resources have been invested in ecological restoration projects across the globe to restore ecosystem integrity. Restoration strategies are often diverse and have been met with mixed success. In this paper, we describe the Chinook salmon (Oncorhynchus tshawytscha) decision-support models developed by the Central Valley Project Improvement Act Science Integration Team as part of a larger structured decision making effort aimed at maximizing natural adult production of Chinook salmon in California’s Central Valley, USA. We then describe the decision analytic tools the stakeholder group used to solve the models and explore model results, including stochastic dynamic programming, forward simulation, proportional scoring, relative loss, expected value of perfect information, response profile analyses, and indifference curves. Using these tools, the stakeholder group was able to develop and evaluate restoration strategies for multiple Chinook salmon runs simultaneously, a first for the restoration program. We found that actions targeted at one run were detrimental to others, which was unexpected. Furthermore, information uncovered during this process was used to direct efforts towards targeted research/monitoring to reduce critical uncertainties in salmon demographic rates and make better restoration decisions moving forward. The decision sciences have established a wide range of analytical tools and approaches to simplify complex problems into key components, and we believe the concepts described in this paper are of great interest and can be applied by many restoration practitioners that undoubtedly face similar difficulties when implementing restoration strategies for complex systems.

California↗

USGS1996

Uncertainty and instream flow standards

Several years ago, Science published an important essay (Ludwig et al. 1993) on the need to confront the scientific uncertainty associated with managing natural resources. The essay did not discuss instream flow standards explicitly, but its arguments apply. At an April 1995 workshop in Davis, California, all 12 participants agreed that currently no scientifically defensible method exists for defining the instream flows needed to protect particular species of fish or aquatic ecosystems (Williams, in press). We also agreed that acknowledging this fact is an essential step in dealing rationally and effectively with the problem. Practical necessity and the protection of fishery resources require that new instream flow standards be established and that existing standards be revised. However, if standards cannot be defined scientifically, how can this be done? We join others in recommending the approach of adaptive management. Applied to instream flow standards, this approach involves at least three elements.

Fisheries↗

USGS2001

Applying the scientific method to small catchment studies: Areview of the Panola Mountain experience

A hallmark of the scientific method is its iterative application to a problem to increase and refine the understanding of the underlying processes controlling it. A successful iterative application of the scientific method to catchment science (including the fields of hillslope hydrology and biogeochemistry) has been hindered by two factors. First, the scale at which controlled experiments can be performed is much smaller than the scale of the phenomenon of interest. Second, computer simulation models generally have not been used as hypothesis-testing tools as rigorously as they might have been. Model evaluation often has gone only so far as evaluation of goodness of fit, rather than a full structural analysis, which is more useful when treating the model as a hypothesis. An iterative application of a simple mixing model to the Panola Mountain Research Watershed is reviewed to illustrate the increase in understanding gained by this approach and to discern general principles that may be applicable to other studies. The lessons learned include the need for an explicitly stated conceptual model of the catchment, the definition of objective measures of its applicability, and a clear linkage between the scale of observations and the scale of predictions. Published in 2001 by John Wiley & Sons. Ltd.

Hydrological Processes↗

USGS2014

A deglacial and Holocene record of climate variability in south-central Alaska from stable oxygen isotopes and plant macrofossils in peat

We used stable oxygen isotopes derived from bulk peat (δ 18 O TOM ), in conjunction with plant macrofossils and previously published carbon accumulation records, in a &sim;14,500 cal yr BP peat core (HT Fen) from the Kenai lowlands in south-central Alaska to reconstruct the climate history of the area. We find that patterns are broadly consistent with those from lacustrine records across the region, and agree with the interpretation that major shifts in δ 18 O TOM values indicate changes in strength and position of the Aleutian Low (AL), a semi-permanent low-pressure cell that delivers winter moisture to the region. We find decreased strength or a more westerly position of the AL (relatively higher δ 18 O TOM values) during the Bølling-Allerød, Holocene Thermal Maximum (HTM), and late Holocene, which also correspond to warmer climate regimes. These intervals coincide with greater peat preservation and enhanced carbon (C) accumulation rates at the HT Fen and with peatland expansion across Alaska. The HTM in particular may have experienced greater summer precipitation as a result of an enhanced Pacific subtropical high, a pattern consistent with modern δ 18 O values for summer precipitation. The combined warm summer temperatures and greater summer precipitation helped promote the observed rapid peat accumulation. A strengthened AL (relatively lower δ 18 O TOM values) is most evident during the Younger Dryas, Neoglaciation, and the Little Ice Age, consistent with lower peat preservation and C accumulation at the HT Fen, suggesting less precipitation reaches the leeward side of the Kenai Mountains during periods of enhanced AL strength. The peatlands on the Kenai Peninsula thrive when the AL is weak and the contribution of summer precipitation is higher, highlighting the importance of precipitation seasonality in promoting peat accumulation. This study demonstrates that δ 18 O TOM values in peat can be applied toward understand large-scale shifts in atmospheric circulation over millennial timescales.

Alaska↗

USGS2025

A method to obtain remotely sensed grain size distributions from nonplanar granular deposits

Constraining the grain size distribution of granular deposits with complex surfaces is difficult with existing approaches. Field and laboratory techniques are time consuming and limited by the maximum grain size that laboratories can accommodate. In this study, we present a new method to identify the coarse fraction of the grain size distribution at a debris-flow fan deposit surveyed with terrestrial laser scanning (TLS) in Glenwood Canyon, Colorado, USA. This method is a novel grain segmentation algorithm developed for application to point cloud data of deposits with complex surfaces and angular grains ranging in size from centimeters to a meter. This approach combines an existing random forest machine learning method with a novel iterative clustering algorithm. We compared the grain size distribution from our algorithm with a Wolman pebble count conducted in the field, and found a root mean squared error of less than 2 cm from the 5th to 95th percentile of the grain size distribution of grains ranging from cobble to boulder sized (6.3–78 cm in our application). Finally, we compared our new algorithm with an existing open-source grain segregation algorithm, and our method outperformed the selected alternative when applied to the debris-flow deposit point cloud.

Colorado↗

USGS2008

Comparative study of transport processes of nitrogen, phosphorus, and herbicides to streams in five agricultural basins, USA

Agricultural chemical transport to surface water and the linkage to other hydrological compartments, principally ground water, was investigated at five watersheds in semiarid to humid climatic settings. Chemical transport was affected by storm water runoff, soil drainage, irrigation, and how streams were linked to shallow ground water systems. Irrigation practices and timing of chemical use greatly affected nutrient and pesticide transport in the semiarid basins. Irrigation with imported water tended to increase ground water and chemical transport, whereas the use of locally pumped irrigation water may eliminate connections between streams and ground water, resulting in lower annual loads. Drainage pathways in humid environments are important because the loads may be transported in tile drains, or through varying combinations of ground water discharge, and overland flow. In most cases, overland flow contributed the greatest loads, but a significant portion of the annual load of nitrate and some pesticide degradates can be transported under base-flow conditions. The highest basin yields for nitrate were measured in a semiarid irrigated system that used imported water and in a stream dominated by tile drainage in a humid environment. Pesticide loads, as a percent of actual use (LAPU), showed the effects of climate and geohydrologic conditions. The LAPU values in the semiarid study basin in Washington were generally low because most of the load was transported in ground water discharge to the stream. When herbicides are applied during the rainy season in a semiarid setting, such as simazine in the California basin, LAPU values are similar to those in the Midwest basins. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Journal of Environmental Quality↗

USGS2008

Measuring the electrical properties of soil using a calibrated ground-coupled GPR system

Traditional methods for estimating vadose zone soil properties using ground penetrating radar (GPR) include measuring travel time, fitting diffraction hyperbolae, and other methods exploiting geometry. Additional processing techniques for estimating soil properties are possible with properly calibrated GPR systems. Such calibration using ground-coupled antennas must account for the effects of the shallow soil on the antenna's response, because changing soil properties result in a changing antenna response. A prototype GPR system using ground-coupled antennas was calibrated using laboratory measurements and numerical simulations of the GPR components. Two methods for estimating subsurface properties that utilize the calibrated response were developed. First, a new nonlinear inversion algorithm to estimate shallow soil properties under ground-coupled antennas was evaluated. Tests with synthetic data showed that the inversion algorithm is well behaved across the allowed range of soil properties. A preliminary field test gave encouraging results, with estimated soil property uncertainties (????) of ??1.9 and ??4.4 mS/m for the relative dielectric permittivity and the electrical conductivity, respectively. Next, a deconvolution method for estimating the properties of subsurface reflectors with known shapes (e.g., pipes or planar interfaces) was developed. This method uses scattering matrices to account for the response of subsurface reflectors. The deconvolution method was evaluated for use with noisy data using synthetic data. Results indicate that the deconvolution method requires reflected waves with a signal/noise ratio of about 10:1 or greater. When applied to field data with a signal/noise ratio of 2:1, the method was able to estimate the reflection coefficient and relative permittivity, but the large uncertainty in this estimate precluded inversion for conductivity. ?? Soil Science Society of America.

Conference Paper↗

USGS1990

Selected translations of the Russian literature on the electrogeochemical sampling technique called CHIM (chastichnoe izvlechennye metallov)

As part of our research into new methods for the assessment of mineral deposits, the U.S. Geological Survey has recently begun investigation of the CHIM method. As part of our studies, translation of a Russian manual on the CHIM methodology and eight articles from the Russian literature were transit ted to provide background for our own research. The translations were done by Earth Science Translation Services of Albuquerque, New Mexico, and are presented as received, without editing on our part. Below is a bibliography of the translated articles. For approximately the past 20 years Russian geoscientists have been applying an electrogeochemical sampling technique given the Russian acronym CHIM, derived from Chastichnoe Izvlechennye Metallov which translates as "partial extraction of metals". In this technique a direct current is introduced into the earth through collector electrodes similar to "porous pots" used in electrical geophysical applications. The solution in the cathode is dilute nitric acid, and current is passed through the cathode for times ranging from 6 hours to 48 hours or more. Electrical connections to the nitric acid are made through an inner conductor that is typically spectroscopically pure graphite. At the cathode, mobile cations collect on the graphite or in the nitric acid solution, both of which serve as the geochemical sampling media. These media are then analyzed by appropriate methods for the ions of interest. In most applications of the CHIM method only mobile cations are sampled, although Russian literature does refer to collection of anions as well. More recently the CHIM method has been applied by the Peoples Republic of China and the Indian Geological Survey. The literature indicates that the method has advantages over other geochemical sampling techniques by providing increased sensitivity to the metals being searched for, especially where deposits are covered by substantial overburden. In some cases success has been claimed with overburden in excess of 500 meters. The technique appears to have been applied principally to exploration for base- and precious-metal deposits, but does not appear to be limited to these. References are made in the literature to its application in the search for nickel, cobalt, molybdenum, uranium, tin, REE, tungsten, berylium, and oil and gas.

Open-File Report↗

USGS2009

Adaptive management of watersheds and related resources

The concept of learning about natural resources through the practice of management has been around for several decades and by now is associated with the term adaptive management. The objectives of this paper are to offer a framework for adaptive management that includes an operational definition, a description of conditions in which it can be usefully applied, and a systematic approach to its application. Adaptive decisionmaking is described as iterative, learning-based management in two phases, each with its own mechanisms for feedback and adaptation. The linkages between traditional experimental science and adaptive management are discussed.

Conference Paper↗

USGS2009

Adaptive management of watersheds and related resources

Conference Paper↗

USGS2026

Erosion and transport of sediments in watersheds of southwest Puerto Rico determined from strontium isotopes and mixing models

Sediment outflow from streams to coastal regions can adversely affect water quality and the health of ecosystems including Puerto Rico's southwestern carbonate platform with shallow marine communities. Knowledge of sediment provenance and erosional areas would aid effective restoration to reduce excessive sedimentation. Strontium (Sr) isotopic ratios ( 87 Sr/ 86 Sr) can be used to differentiate between sediment eroded into streams from different lithologies, or rock types, and used in mixing models to estimate proportions of source materials in downstream mixtures. The goal of this study was to use Sr isotopes to differentiate between river sediments in drainages with distinct geologies and present a case study where Sr isotope mixing models are used to identify sediment sourcing to Río Loco and Bahía de Guánica, a priority watershed of the U.S. Coral Reefs Task Force. For the Río Loco watershed, model results indicate that serpentinites in the uplands contributed approximately 71 % of sediment to Bahía de Guánica. About 21 % of sediment was from trachy-andesitic basalts in the foothills, and the remaining 8 % originated from sources on the coastal plain. Neither the uppermost headwater region of Río Loco, the Canal Principal De Riego Valle De Lajas, nor the tributary Quebrada Susúa appeared to be significant sources of sediment to Río Loco's mainstem or Bahía de Guánica at the time of the study. Our results demonstrate that sediment from the serpentinite-bearing areas of Río Loco watershed was effectively transported to the lowlands, which then discharge into Guánica Bay, and highlight the potential use of Sr isotopes as tracers of sediment provenance. This will, in turn, enable better science-based restoration efforts aimed at reducing terrestrial sediment erosion and impacts to marine ecosystems.

Puerto Rico↗

USGS2011

Estimating site occupancy rates for aquatic plants using spatial sub-sampling designs when detection probabilities are less than one

Estimation of site occupancy rates when detection probabilities are <1 is well established in wildlife science. Data from multiple visits to a sample of sites are used to estimate detection probabilities and the proportion of sites occupied by focal species. In this article we describe how site occupancy methods can be applied to estimate occupancy rates of plants and other sessile organisms. We illustrate this approach and the pitfalls of ignoring incomplete detection using spatial data for 2 aquatic vascular plants collected under the Upper Mississippi River's Long Term Resource Monitoring Program (LTRMP). Site occupancy models considered include: a naïve model that ignores incomplete detection, a simple site occupancy model assuming a constant occupancy rate and a constant probability of detection across sites, several models that allow site occupancy rates and probabilities of detection to vary with habitat characteristics, and mixture models that allow for unexplained variation in detection probabilities. We used information theoretic methods to rank competing models and bootstrapping to evaluate the goodness-of-fit of the final models. Results of our analysis confirm that ignoring incomplete detection can result in biased estimates of occupancy rates. Estimates of site occupancy rates for 2 aquatic plant species were 19–36% higher compared to naive estimates that ignored probabilities of detection <1. Simulations indicate that final models have little bias when 50 or more sites are sampled, and little gains in precision could be expected for sample sizes >300. We recommend applying site occupancy methods for monitoring presence of aquatic species.

Aquatic Botany↗

USGS2002

Geochemistry of fluid phases and sediments: Relevance to hydrothermal circulation in Middle Valley, ODP Legs 139 and 169

Geochemical and isotopic studies of pore fluids and solid phases recovered from the Dead Dog and Bent Hill hydrothermal sites in Middle Valley (Ocean Drilling Program Leg 169) have been compared with similar data obtained previously from these sites during Ocean Drilling Program Leg 139. Although generally the hydrothermal systems reflect non-steady state conditions, the data allow an assessment of the history of the hydrothermal processes. Sediment K/A1 ratios as well as the distribution of anhydrite in the sediments suggest that the Dead Dog hydrothermal field has been, and still is, active. In contrast, similar data in the Bent Hill hydrothermal field indicate a waning of hydrothermal activity. Pore fluid and hydrothermal vent data in the Dead Dog hydrothermal field are similar in nature to the data collected during ODP Leg 139. In the area of the Bent Hill sulfide deposit, however, the pore water data indicate that recent wholesale flushing of the sediment column with relatively unaltered seawater has obliterated a previous record of hydrothermal activity in the pore fluids. Data from the deepest part of Hole 1035A in the Bent Hill locality show the presence of hydrothermal fluids at greater depths in this area. This suggests the origin of the hydrothermal fluids found to be emanating from Hole 1035F, which constitutes one of the first man made hydrothermal vents in the Middle Valley hydrothermal system. Similarly, CORKed Hole 858G, because of seal failures, has acted as a hydrothermal vent, with sulfide deposits forming inside the CORK. ?? 2002 Elsevier Science Ltd. All rights reserved.

Applied Geochemistry↗

USGS2015

Predicting spatial distribution of postfire debris flows and potential consequences for native trout in headwater streams

Habitat fragmentation and degradation and invasion of nonnative species have restricted the distribution of native trout. Many trout populations are limited to headwater streams where negative effects of predicted climate change, including reduced stream flow and increased risk of catastrophic fires, may further jeopardize their persistence. Headwater streams in steep terrain are especially susceptible to disturbance associated with postfire debris flows, which have led to local extirpation of trout populations in some systems. We conducted a reach-scale spatial analysis of debris-flow risk among 11 high-elevation watersheds of the Colorado Rocky Mountains occupied by isolated populations of Colorado River Cutthroat Trout (Oncorhynchus clarkii pleuriticus). Stream reaches at high risk of disturbance by postfire debris flow were identified with the aid of a qualitative model based on 4 primary initiating and transport factors (hillslope gradient, flow accumulation pathways, channel gradient, and valley confinement). This model was coupled with a spatially continuous survey of trout distributions in these stream networks to assess the predicted extent of trout population disturbances related to debris flows. In the study systems, debris-flow potential was highest in the lower and middle reaches of most watersheds. Colorado River Cutthroat Trout occurred in areas of high postfire debris-flow risk, but they were never restricted to those areas. Postfire debris flows could extirpate trout from local reaches in these watersheds, but trout populations occupy refugia that should allow recolonization of interconnected, downstream reaches. Specific results of our study may not be universally applicable, but our risk assessment approach can be applied to assess postfire debris-flow risk for stream reaches in other watersheds.

Colorado↗

USGS2010

Lunar highland meteorite Dhofar 026 and Apollo sample 15418: Two strongly shocked, partially melted, granulitic breccias

Studies of lunar meteorite Dhofar 026, and comparison to Apollo sample 15418, indicate that Dhofar 026 is a strongly shocked granulitic breccia (or a fragmental breccia consisting almost entirely of granulitic breccia clasts) that experienced considerable post-shock heating, probably as a result of diffusion of heat into the rock from an external, hotter source. The shock converted plagioclase to maskelynite, indicating that the shock pressure was between 30 and 45 GPa. The post-shock heating raised the rock's temperature to about 1200 °C; as a result, the maskelynite devitrified, and extensive partial melting took place. The melting was concentrated in pyroxene-rich areas; all pyroxene melted. As the rock cooled, the partial melts crystallized with fine-grained, subophitic-poikilitic textures. Sample 15418 is a strongly shocked granulitic breccia that had a similar history, but evidence for this history is better preserved than in Dhofar 026. The fact that Dhofar 026 was previously interpreted as an impact melt breccia underscores the importance of detailed petrographic study in interpretation of lunar rocks that have complex textures. The name “impact melt” has, in past studies, been applied only to rocks in which the melt fraction formed by shock-induced total fusion. Recently, however, this name has also been applied to rocks containing melt formed by heating of the rocks by conductive heat transfer, assuming that impact is the ultimate source of the heat. We urge that the name “impact melt” be restricted to rocks in which the bulk of the melt formed by shock-induced fusion to avoid confusion engendered by applying the same name to rocks melted by different processes.

Meteoritics and Planetary Science↗

USGS2009

Elemental signatures in otoliths of hatchery rainbow trout (Oncorhynchus mykiss): Distinctiveness and utility fo detecting origins and movement

Otolith chemistry in freshwater has considerable potential to reveal patterns of origin and movement, which would benefit traditional fisheries management and provide a valuable tool to curb the spread of invasive and illicitly stocked species. We evaluated the relationship between otolith and water chemistry for five markers (Ba/Ca, Mn/Ca, Sr/ Ca, Zn/Ca, and 87 Sr/ 86 Sr) in rainbow trout (Oncorhynchus mykiss) using the existing hatchery system in Colorado and Wyoming, USA, to provide controlled, seminatural conditions. Otolith Ba/Ca, Sr/Ca, and 87 Sr/ 86 Sr reflected ambient levels, whereas Mn/Ca and Zn/Ca did not. Using only the markers correlated with water chemistry, we classified fish to their hatchery of origin with up to 96% accuracy when element and isotope data were used together. Large changes in 87Sr/ Sr were evident in otolith transects, although subtler changes in Sr/Ca were also detectable. Our results suggest the relatively few otolith markers that reflect ambient chemistry can discriminate among locations and track movements well enough to provide valuable insight in a variety of applied contexts.

Canadian Journal of Fisheries and Aquatic Sciences↗