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USGS2010

Site-occupancy distribution modeling to correct population-trend estimates derived from opportunistic observations

Species' assessments must frequently be derived from opportunistic observations made by volunteers (i.e., citizen scientists). Interpretation of the resulting data to estimate population trends is plagued with problems, including teasing apart genuine population trends from variations in observation effort. We devised a way to correct for annual variation in effort when estimating trends in occupancy (species distribution) from faunal or floral databases of opportunistic observations. First, for all surveyed sites, detection histories (i.e., strings of detection-nondetection records) are generated. Within-season replicate surveys provide information on the detectability of an occupied site. Detectability directly represents observation effort; hence, estimating detectablity means correcting for observation effort. Second, site-occupancy models are applied directly to the detection-history data set (i.e., without aggregation by site and year) to estimate detectability and species distribution (occupancy, i.e., the true proportion of sites where a species occurs). Site-occupancy models also provide unbiased estimators of components of distributional change (i.e., colonization and extinction rates). We illustrate our method with data from a large citizen-science project in Switzerland in which field ornithologists record opportunistic observations. We analyzed data collected on four species: the widespread Kingfisher (Alcedo atthis. ) and Sparrowhawk (Accipiter nisus. ) and the scarce Rock Thrush (Monticola saxatilis. ) and Wallcreeper (Tichodroma muraria. ). Our method requires that all observed species are recorded. Detectability was <1 and varied over the years. Simulations suggested some robustness, but we advocate recording complete species lists (checklists), rather than recording individual records of single species. The representation of observation effort with its effect on detectability provides a solution to the problem of differences in effort encountered when extracting trend information from haphazard observations. We expect our method is widely applicable for global biodiversity monitoring and modeling of species distributions. ?? 2010 Society for Conservation Biology.

Conservation Biology↗

USGS2023

Interlaboratory comparison of testing hydraulic, elastic, and failure properties in compression: Lessons learned

Many geoscientific problems require us to exploit synergies of experimental and numerical approaches, which in turn lead to questions regarding the significance of experimental details for validation of numerical codes. We report results of an interlaboratory comparison regarding experimental determination of mechanical and hydraulic properties of samples from five rock types, three sandstone varieties with porosities ranging from 5% to 20%, a marble, and a granite. The objective of this study was to build confidence in the participating laboratories’ testing approaches and to establish tractable standards for several physical properties of rocks. We addressed the issue of sample-to-sample variability by investigating the variability of basic physical properties of samples of a particular rock type and by performing repeat tests. Compressive strength of the different rock types spans an order of magnitude and shows close agreement between the laboratories. However, differences among stress–strain relations indicate that the external measurement of axial displacement and the determination of system stiffness require special attention, apparently more so than the external load measurement. Furthermore, post-failure behavior seems to exhibit some machine-dependence. The different methods used for the determination of hydraulic permeability, covering six orders of magnitude for the sample suite, yield differences in absolute values and pressure dependence for some rocks but not for others. The origin of the differences in permeability, in no case exceeding an order of magnitude, correlate with the compressive strength and potentially reflect a convolution of end plug–sample interaction, sample-to-sample variability, heterogeneity on sample scale, and/or anisotropy, the last two aspects are notably not accounted for by the applied evaluation procedures. Our study provides an extensive data set apt for “benchmarking” considerations, be it regarding new laboratory equipment or numerical modeling approaches.

Environmental Earth Sciences↗

USGS2004

Tidal oscillation of sediment between a river and a bay: A conceptual model

A conceptual model of fine sediment transport between a river and a bay is proposed, based on observations at two rivers feeding the same bay. The conceptual model consists of river, transitional, and bay regimes. Within the transitional regime, resuspension, advection, and deposition create a mass of sediment that oscillates landward and seaward. While suspended, this sediment mass forms an estuarine turbidity maximum. At slack tides this sediment mass temporarily deposits on the bed, creating landward and seaward deposits. Tidal excursion and slack tide deposition limit the range of the sediment mass. To verify this conceptual model, data from two small tributary rivers of San Pablo Bay are presented. Tidal variability of suspended-sediment concentration markedly differs between the landward and seaward deposits, allowing interpretation of the intratidal movement of the oscillating sediment mass. Application of this model in suitable estuaries will assist in numerical model calibration as well as in data interpretation. A similar model has been applied to some larger-scale European estuaries, which bear a geometric resemblance to the systems analyzed in this study. ?? 2004 Elsevier Ltd. All rights reserved.

California↗

USGS2025

Characterizing pyrethroid and fipronil concentrations in biosolids

Pesticides are prevalent in wastewater, yet few studies have measured pesticides in biosolids and aqueous media from samples collected concurrently. Seventeen California wastewater treatment plants (WWTPs) were sampled in May 2020. Biosolids samples were analyzed for 27 analytes, and paired aqueous samples (influent and effluent) were analyzed for 23 analytes. Analytes included fipronil and its transformation products (fiproles), pyrethroids, novaluron, and several other pesticides with down-the-drain transport potential. Of the 27 compounds analyzed in biosolids samples, 16 were detected in at least one sample, and 10 had a detection frequency (DF) of at least 25 %. Fipronil sulfone, fipronil sulfide, and fipronil were the most frequently detected fiproles (DF = 100 %, 94 %, and 67 %, respectively); permethrin was the most frequently detected pyrethroid (DF = 100 %), followed by bifenthrin (DF = 94 %), cyhalothrin (DF = 89 %), and etofenprox (DF = 78 %). To elucidate fipronil transformation pathways within the treatment system, data from the three sample types were compared; findings were generally consistent with transformation pathways reported previously (e.g., some fiproles were rarely detected in influent or biosolids, but frequently detected in effluent, indicating their formation during the treatment process). No correlations were found between WWTP characteristics and pesticide concentrations in biosolids. The fraction of organic carbon ( f OC ) of each biosolids sample was measured, and a statistically significant negative correlation was observed between f OC and some fiproles, but not fipronil; possible explanations are discussed. Additional analysis for two major agricultural pesticides (bifenthrin and permethrin) indicated that estimated mass loads of these pesticides in biosolids applied to land as a soil amendment are minimal (approximately 2 to 3 orders of magnitude lower) compared to inputs from agricultural applications. This study provides insight on the magnitude of pesticides entering the environment via land-applied biosolids; existing regulations surrounding agricultural pesticide applications are expected to also be protective of the relatively low inputs from biosolids.

Science of the Total Environment↗

USGS2011

Workshop discusses community models for coastal sediment transport

Numerical models of coastal sediment transport are increasingly used to address problems ranging from remediation of contaminated sediments, to siting of sewage outfalls and disposal sites, to evaluating impacts of coastal development. They are also used as a test bed for sediment-transport algorithms, to provide realistic settings for biological and geochemical models, and for a variety of other research, both fundamental and applied. However, there are few full-featured, publicly available coastal sediment-transport models, and fewer still that are well tested and have been widely applied. This was the motivation for a workshop in Woods Hole, Massachusetts, on June 22–23, 2000, that explored the establishment of community models for coastal sediment-transport processes.

Eos Science News↗

USGS2021

A metapopulation model of social group dynamics and disease applied to Yellowstone wolves

The population structure of social species has important consequences for both their demography and transmission of their pathogens. We develop a metapopulation model that tracks two key components of a species’ social system: average group size and number of groups within a population. While the model is general, we parameterize it to mimic the dynamics of the Yellowstone wolf population and two associated pathogens: sarcoptic mange and canine distemper. In the initial absence of disease, we show that group size is mainly determined by the birth and death rates and the rates at which groups fission to form new groups. The total number of groups is determined by rates of fission and fusion, as well as environmental resources and rates of intergroup aggression. Incorporating pathogens into the models reduces the size of the host population, predominantly by reducing the number of social groups. Average group size responds in more subtle ways: infected groups decrease in size, but uninfected groups may increase when disease reduces the number of groups and thereby reduces intraspecific aggression. Our modeling approach allows for easy calculation of prevalence at multiple scales (within group, across groups, and population level), illustrating that aggregate population-level prevalence can be misleading for group-living species. The model structure is general, can be applied to other social species, and allows for a dynamic assessment of how pathogens can affect social structure and vice versa.

Proceedings of the National Academy of Sciences↗

USGS2007

Revised landsat-5 thematic mapper radiometric calibration

Effective April 2, 2007, the radiometric calibration of Landsat-5 (L5) Thematic Mapper (TM) data that are processed and distributed by the U.S. Geological Survey (USGS) Center for Earth Resources Observation and Science (EROS) will be updated. The lifetime gain model that was implemented on May 5, 2003, for the reflective bands (1-5, 7) will be replaced by a new lifetime radiometric-calibration curve that is derived from the instrument's response to pseudoinvariant desert sites and from cross calibration with the Landsat-7 (L7) Enhanced TM Plus (ETM+). Although this calibration update applies to all archived and future L5 TM data, the principal improvements in the calibration are for the data acquired during the first eight years of the mission (1984-1991), where the changes in the instrument-gain values are as much as 15%. The radiometric scaling coefficients for bands 1 and 2 for approximately the first eight years of the mission have also been changed. Users will need to apply these new coefficients to convert the calibrated data product digital numbers to radiance. The scaling coefficients for the other bands have not changed.

IEEE Geoscience and Remote Sensing Letters↗

USGS2022

A framework to integrate innovations in invasion science for proactive management

Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.

Biological Reviews↗

USGS2020

Remarkable response of native fishes to invasive trout suppression varies with trout density, temperature, and annual hydrology

Recovery of imperiled fishes can be achieved through suppression of invasives, but outcomes may vary with environmental conditions. We studied the response of imperiled desert fishes to an invasive brown ( Salmo trutta ) and rainbow trout ( Oncorhynchus mykiss ) suppression program in a Colorado River tributary, with natural flow and longitudinal variation in thermal characteristics. We investigated trends in fish populations related to suppression and tested hypotheses about the impacts of salmonid densities, hydrologic variation, and spatial–thermal gradients on the distribution and abundance of native fish species using zero-inflated generalized linear mixed effects models. Between 2012 and 2018, salmonids declined 89%, and native fishes increased dramatically (∼480%) once trout suppression surpassed ∼60%. Temperature and trout density were consistently retained in the top models predicting the abundance and distribution of native fishes. The greatest increases occurred in warmer reaches and in years with spring flooding. Surprisingly, given the evolution of native fishes in disturbance-prone systems, intense, monsoon-driven flooding limited native fish recruitment. Applied concertedly, invasive species suppression and efforts to mimic natural flow and thermal regimes may allow rapid and widespread native fish recovery.

Arizona↗

USGS2021

Knowledge gaps update to the 2019 IPCC special report on the ocean and cryosphere: Prospects to refine coastal flood hazard assessments and adaptation strategies with at-risk communities of Alaska

This article reviews the status of knowledge gaps and co-production process challenges that impede coastal flood hazard resilience planning in communities of northwestern Alaska, where threat levels are high. Discussion focuses on the state of knowledge arising after preparation of the 2019 IPCC Special Report on the Ocean and Cryosphere in a Changing Climate and highlights prospects to address urgent needs. The intent is to identify some key steps necessary to advance the integration of relevant multidisciplinary observations with flood modeling and infrastructure mapping to co-produce new online hazard and risk assessment tools that inform local community planning and improve science collaboration among Federal, state, and regional partners for enhanced pre-storm preparations and post-storm recovery, including partial or complete relocation. By focusing coastal data integration for delivery of priority geospatial hazard map products through a consistent yet customized approach to adaptation planning, the broad collaborative effort in Alaska may yield a path of stakeholder service delivery that can be applied to many Arctic communities and other vulnerable regions of the world.

Frontiers in Climate↗

USGS2002

Groundwater contamination downstream of a contaminant penetration site. II. Horizontal penetration of the contaminant plume

Part I of this study (Rubin, H.; Buddemeier, R.W. Groundwater Contamination Downstream of a Contaminant Penetration Site Part 1: Extension-Expansion of the Contaminant Plume. J. of Environmental Science and Health Part A (in press).) addressed cases, in which a comparatively thin contaminated region represented by boundary layers (BLs) developed within the freshwater aquifer close to contaminant penetration site. However, at some distance downstream from the penetration site, the top of the contaminant plume reaches the top or bottom of the aquifer. This is the location of the "attachment point," which comprises the entrance cross section of the domain evaluated by the present part of the study. It is shown that downstream from the entrance cross section, a set of two BLs develop in the aquifer, termed inner and outer BLs. It is assumed that the evaluated domain, in which the contaminant distribution gradually becomes uniform, can be divided into two sections, designated: (a) the restructuring section, and (b) the establishment section. In the restructuring section, the vertical concentration gradient leads to expansion of the inner BL at the expense of the outer BL, and there is almost no transfer of contaminant mass between the two layers. In the establishment section, each of the BLs occupies half of the aquifer thickness, and the vertical concentration gradient leads to transfer of contaminant mass from the inner to the outer BL. By use of BL approximations, changes of salinity distribution in the aquifer are calculated and evaluated. The establishment section ends at the uniformity point, downstream from which the contaminant concentration profile is practically uniform. The length of the restructuring section, as well as that of the establishment section, is approximately proportional to the aquifer thickness squared, and is inversely proportional to the transverse dispersivity. The study provides a convenient set of definitions and terminology that are helpful in visualizing the gradual development of uniform contaminant concentration distribution in an aquifer subject to contaminant plume penetration. The method developed in this study can be applied to a variety of problems associated with groundwater quality, such as initial evaluation of field data, design of field data collection, the identification of appropriate boundary conditions for numerical models, selection of appropriate numerical modeling approaches, interpretation and evaluation of field monitoring results, etc.

Journal of Environmental Science and Health - Part↗

USGS1980

Examples of the use of earth-science information by decisionmakers in the San Francisco Bay region, California

In the six examples discussed and illustrated here, innovative decisionmakers -- public and private -- have used earth-science information to avoid areas with geologic hazards, protect natural resources, and reduce possible property damage in the San Francisco Bay region. The examples show how: 1) development in fault-rupture areas is regulated, 2) potential waste-disposal sites are identified, 3) aquatic and wildlife habitats are protected, 4) site investigations are required in hazardous areas, 5) supplemental building standards can be applied to unstable baylands, and 6) hazards are disclosed to real-estate buyers.

California↗

USGS1982

The UThPb age of equilibrated L chondrites and a solution to the excess radiogenic Pb problem in chondrites

U, Th, and Pb analyses of whole-rock and troilite separates from seven L chondrites suggest that the excess radiogenic Pb relative to U and the large variations in Pb Pb model ages commonly observed in chondritic meteorites are largely due to terrestrial Pb contamination induced prior to analyses. Using the Pb isotopic composition of troilite separates to calculate the isotopic composition of the Pb contaminants, the whole-rock data have been corrected for pre-analysis terrestrial Pb contamination. Two approaches have been used: (1) the chondrite-troilite apparent initial Pb isotopic compositions were used to approximate the mixture of indigenous intial Pb and terrestrial Pb in the whole-rock sample, and (2) a single-stage (concordant) model was applied using the assumption that the excess radiogenic Pb in these samples was terrestrial. Data for L5 and L6 chondrites yield a 4551 ± 7My age using the former correction and a 4550 ± 5My age using the latter one.

Earth and Planetary Science Letters↗

USGS2024

Applying mark-resight, count, and telemetry data to estimate effective sampling area and fish density with stationary underwater cameras

Accurate estimates of abundance and density for geographically open populations must account for the effective sampling area (ESA) of sampling gears. We describe a Marked N-Mixture model to estimate ESA and density (number of individuals/unit area) from repeated counts of unmarked and marked individuals, integrating mark-resight, camera counts, and telemetry data of red snapper ( Lutjanus campechanus ) at a 1.6 km 2 reef off North Carolina, USA. Cameras recorded observations of unmarked and marked individuals, whereas telemetry data indicated the number of tagged fish present on the reef. We estimated density (95 individuals/km 2 , 95%CI: 58–149), ESA (which was lower when current direction was towards the camera), detection probability (0.06, 95%CI: 0.03–0.09), and covariate relationships. Simulation studies under different scenarios of data quality and space use identified positive bias in density estimates from N-mixture models due to fish movement. In contrast, the Marked N-Mixture model returned unbiased estimates of density, ESA, and detection parameters, and appears to be a more robust method for modeling density given the data available for this analysis. This approach can be applied to other populations where count and telemetry data overlap in space and time.

North Carolina↗

USGS2008

Development and evaluation of geochemical methods for the sourcing of archaeological maize

Strontium (Sr)-isotope values on bone from deer mice pairs from 12 field sites in the Chaco Canyon area, New Mexico, were compared with isotope values of synthetic soil waters from the same fields. The data indicate that mice obtain Sr from near-surface sources and that soil samples collected at depths ranging from 25 to 95 cm contain Sr that is more accessible to the deep roots of maize; thus, synthetic soil solutions provide better data for the sourcing of archaeological maize. However, the Sr-isotope composition of mice may be more valuable in sourcing archaeological remains of animals such as rabbit, turkey, and deer. In a separate study, five Native American maize (Zea mays L. ssp. mays) accessions grown out at New Mexico State University Agricultural Science Center, Farmington, New Mexico were used to determine if soil-water metal pairs partition systematically into cobs and kernels. The sampled maize included landraces from three Native American groups (Acoma, Hopi, Zuni) that still occupy the Four Corners area. Two cobs each were picked from 10 plants of each landrace. Partitioning of the Ba/Mn, Ba/Sr, Ca/Sr, and K/Rb metal pairs from the soil water to the cob appears to behave in a systematic fashion. In addition, 51 rare earth element (REE) pairs also appear to systematically partition from the soil water into cobs; however, the ratios of the REE dissolved in the soil waters are relatively invariant; therefore, the distribution coefficients that describe the partitioning of REE from the soil water to the cob may not apply to archeological cobs grown under chemically heterogeneous conditions. Partitioning of Ba/Rb, Ba/Sr, Mg/P, and Mn/P metal pairs from the soil water to kernels also behaves in a systematic fashion. Given that modern Native American landraces were grown under optimal environmental conditions that may not have been duplicated by prehistoric Native Americans, the distribution coefficients obtained in this study should be used with caution. ?? 2007 Elsevier Ltd. All rights reserved.

Journal of Archaeological Science↗

USGS2019

One hundred pressing questions on the future of global fish migration science, conservation, and policy

Migration is a widespread but highly diverse component of many animal life histories. Fish migrate throughout the world's oceans, within lakes and rivers, and between the two realms, transporting matter, energy, and other species (e.g., microbes) across boundaries. Migration is therefore a process responsible for myriad ecosystem services. Many human populations depend on the presence of predictable migrations of fish for their subsistence and livelihoods. Although much research has focused on fish migration, many questions remain in our rapidly changing world. We assembled a diverse team of fundamental and applied scientists who study fish migrations in marine and freshwater environments to identify pressing unanswered questions. Our exercise revealed questions within themes related to understanding the migrating individual's internal state, navigational mechanisms, locomotor capabilities, external drivers of migration, the threats confronting migratory fish including climate change, and the role of migration. In addition, we identified key requirements for aquatic animal management, restoration, policy, and governance. Lessons revealed included the difficulties in generalizing among species and populations, and in understanding the levels of connectivity facilitated by migrating fishes. We conclude by identifying priority research needed for assuring a sustainable future for migratory fishes.

Frontiers in Ecology and Evolution↗

USGS2000

Lithofacies identification using multiple adaptive resonance theory neural networks and group decision expert system

Lithofacies identification supplies qualitative information about rocks. Lithofacies represent rock textures and are important components of hydrocarbon reservoir description. Traditional techniques of lithofacies identification from core data are costly and different geologists may provide different interpretations. In this paper, we present a low-cost intelligent system consisting of three adaptive resonance theory neural networks and a rule-based expert system to consistently and objectively identify lithofacies from well-log data. The input data are altered into different forms representing different perspectives of observation of lithofacies. Each form of input is processed by a different adaptive resonance theory neural network. Among these three adaptive resonance theory neural networks, one neural network processes the raw continuous data, another processes categorial data, and the third processes fuzzy-set data. Outputs from these three networks are then combined by the expert system using fuzzy inference to determine to which facies the input data should be assigned. Rules are prioritized to emphasize the importance of firing order. This new approach combines the learning ability of neural networks, the adaptability of fuzzy logic, and the expertise of geologists to infer facies of the rocks. This approach is applied to the Appleton Field, an oil field located in Escambia County, Alabama. The hybrid intelligence system predicts lithofacies identity from log data with 87.6% accuracy. This prediction is more accurate than those of single adaptive resonance theory networks, 79.3%, 68.0% and 66.0%, using raw, fuzzy-set, and categorical data, respectively, and by an error-backpropagation neural network, 57.3%. (C) 2000 Published by Elsevier Science Ltd. All rights reserved.

Computers & Geosciences↗

USGS2021

Quantifying slopes as a driver of forest to marsh conversion using geospatial techniques: Application to Chesapeake Bay coastal-plain, USA

Coastal salt marshes, which provide valuable ecosystem services such as flood mitigation and carbon sequestration, are threatened by rising sea level. In response, these ecosystems migrate landward, converting available upland into salt marsh. In the coastal-plain surrounding Chesapeake Bay, United States, conversion of coastal forest to salt marsh is well-documented and may offset salt marsh loss due to sea level rise, sediment deficits, and wave erosion. Land slope at the marsh-forest boundary is an important factor determining migration likelihood, however, the standard method of using field measurements to assess slope across the marsh-forest boundary is impractical on the scale of an estuary. Therefore, we developed a general slope quantification method that uses high resolution elevation data and a repurposed shoreline analysis tool to determine slope along the marsh-forest boundary for the entire Chesapeake Bay coastal-plain and find that less than 3% of transects have a slope value less than 1%; these low slope environments offer more favorable conditions for forest to marsh conversion. Then, we combine the bay-wide slope and elevation data with inundation modeling from Hurricane Isabel to determine likelihood of coastal forest conversion to salt marsh. This method can be applied to local and estuary-scale research to support management decisions regarding which upland forested areas are more critical to preserve as available space for marsh migration.

Delaware, Maryland, Virginia↗