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Introduction to the U.S. Geological Survey National Water-Quality Assessment (NAWQA) of ground-water quality trends and comparison to other national programs

Assessment of temporal trends in national ground-water quality networks are rarely published in scientific journals. This is partly due to the fact that long-term data from these types of networks are uncommon and because many national monitoring networks are not driven by hypotheses that can be easily incorporated into scientific research. The U.S. Geological Survey (USGS) National Water-Quality Assessment Program (NAWQA) since 1991 has to date (2006) concentrated on occurrence of contaminants because sufficient data for trend analysis is only just becoming available. This paper introduces the first set of trend assessments from NAWQA and provides an assessment of the success of the program. On a national scale, nitrate concentrations in ground water have generally increased from 1988 to 2004, but trends in pesticide concentrations are less apparent. Regionally, the studies showed high nitrate concentrations and frequent pesticide detections are linked to agricultural use of fertilizers and pesticides. Most of these areas showed increases in nitrate concentration within the last decade, and these increases are associated with oxic-geochemical conditions and well-drained soils. The current NAWQA plan for collecting data to define trends needs to be constantly reevaluated to determine if the approach fulfills the expected outcome. To assist this evaluation, a comparison of NAWQA to other national ground-water quality programs was undertaken. The design and spatial extent of each national program depend on many factors, including current and long-term budgets, purpose of the program, size of the country, and diversity of aquifer types. Comparison of NAWQA to nine other national programs shows a great diversity in program designs, but indicates that different approaches can achieve similar and equally important goals. Copyright ?? 2008 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. All rights reserved.

Conference Paper

Mars Exploration Rover Navigation Camera in-flight calibration

The Navigation Camera (Navcam) instruments on the Mars Exploration Rover (MER) spacecraft provide support for both tactical operations as well as scientific observations where color information is not necessary: large-scale morphology, atmospheric monitoring including cloud observations and dust devil movies, and context imaging for both the thermal emission spectrometer and the in situ instruments on the Instrument Deployment Device. The Navcams are a panchromatic stereoscopic imaging system built using identical charge-coupled device (CCD) detectors and nearly identical electronics boards as the other cameras on the MER spacecraft. Previous calibration efforts were primarily focused on providing a detailed geometric calibration in line with the principal function of the Navcams, to provide data for the MER navigation team. This paper provides a detailed description of a new Navcam calibration pipeline developed to provide an absolute radiometric calibration that we estimate to have an absolute accuracy of 10% and a relative precision of 2.5%. Our calibration pipeline includes steps to model and remove the bias offset, the dark current charge that accumulates in both the active and readout regions of the CCD, and the shutter smear. It also corrects pixel-to-pixel responsivity variations using flat-field images, and converts from raw instrument-corrected digital number values per second to units of radiance (W m-2 nm-1 sr-1), or to radiance factor (I/F). We also describe here the initial results of two applications where radiance-calibrated Navcam data provide unique information for surface photometric and atmospheric aerosol studies. Copyright 2008 by the American Geophysical Union.

Journal of Geophysical Research E: Planets

Genetic basis of thiaminase I activity in a vertebrate, zebrafish Danio rerio

Thiamine (vitamin B 1 ) metabolism is an important driver of human and animal health and ecological functioning. Some organisms, including species of ferns, mollusks, and fish, contain thiamine-degrading enzymes known as thiaminases, and consumption of these organisms can lead to thiamine deficiency in the consumer. Consumption of fish containing thiaminase has led to elevated mortality and recruitment failure in farmed animals and wild salmonine populations around the world. In the North American Great Lakes, consumption of the non-native prey fish alewife ( Alosa pseudoharengus ) by native lake trout ( Salvelinus namaycush ) led to thiamine deficiency in the trout, contributed to elevated fry mortality, and impeded natural population recruitment. Several thiaminases have been genetically characterized in bacteria and unicellular eukaryotes, and the source of thiaminase in multicellular organisms has been hypothesized to be gut microflora. In an unexpected discovery, we identified thiaminase I genes in zebrafish ( Danio rerio ) with homology to bacterial tenA thiaminase II. The biochemical activity of zebrafish thiaminase I (GenBank NP_001314821.1) was confirmed in a recombinant system. Genes homologous to the zebrafish tenA-like thiaminase I were identified in many animals, including common carp ( Cyprinus carpio ), zebra mussel ( Dreissena polymorpha ) and alewife. Thus, the source of thiaminase I in alewife impacting lake trout populations is likely to be de novo synthesis.

Scientific Reports

The saltiest springs in the Sierra Nevada, California

The five saltiest springs in the Sierra Nevada in California are found between 38.5° and 38.8° N. latitude, on the South Fork American River; on Caples Creek, a tributary of the Silver Fork American River; and on the North Fork Mokelumne River. The springs issue from Cretaceous granitic rocks in the bottoms of these major canyons, between 1,200- and 2,200-m elevation. All of these springs were well known to Native Americans, who excavated meter-sized basins in the granitic rock, within which they produced salt by evaporation near at least four of the five spring sites. The spring waters are dominated by Cl, Na, and Ca; are enriched relative to seawater in Ca, Li, and As; and are depleted in SO 4 , Mg, and K. Tritium analyses indicate that the spring waters have had little interaction with rainfall since about 1954. The waters are apparently an old groundwater of meteoric origin that resided at depth before moving up along fractures to the surface of the exhumed granitic rocks. However, along the way these waters incorporated salts from depth, the origin of which could have been either from marine sedimentary rocks intruded by the granitic magmas or from fluid inclusions in the granitic rocks. Prolonged storage at depth fostered water-rock interactions that undoubtedly modified the fluid compositions.

California

Environmental characterization of Blue Mesa Reservoir and potential causes of and management strategies for harmful algal blooms, 1970 through 2023, Curecanti National Recreation Area, Colorado

Blue Mesa Reservoir, in the Curecanti National Recreation Area, is the largest storage reservoir in Colorado and consists of three distinct basins: Iola (the shallowest), Cebolla, and Sapinero. After algal toxins were first documented in Iola basin in 2018, the U.S. Geological Survey began a study in cooperation with the National Park Service, Colorado River Water Conservation District, Upper Gunnison River Water Conservancy District, Gunnison County, Project 7 Water Authority, and Uncompahgre Valley Water Users Association to better understand occurrence of toxic cyanobacteria harmful algal blooms (cyanoHABs) and identify possible causal mechanisms to potentially inform management strategies. Toxic cyanoHABS occurred when the algal toxin microcystin exceeded a concentration of 8 micrograms per liter primarily in Iola basin in 2018 and 2020–22, years having some of the lowest reservoir water-level elevations (reservoir levels) since 1984. The toxic cyanoHABs started in mid-September and continued through the fall months. Algal abundance was greatest in Iola basin compared to Cebolla and Sapinero basins, with Aphanizomenon , a toxin-producing cyanobacterium, being the most abundant. During blooms, enhanced algal photosynthesis caused elevated pH and dissolved oxygen concentrations especially in Iola basin. Continuous monitor data in Iola basin indicated peaks in phycocyanin fluorescence, pH, and dissolved oxygen concentration that preceded the onset of toxic cyanoHABs by about 2 weeks potentially indicating a useful early warning monitoring strategy for future response to toxic cyanoHABs. Long-term trends showed increases in mean air and surface-water temperatures and chlorophyll- a concentrations in the reservoir but no change in nutrient inputs from major tributaries. In Iola basin, reservoir level was positively correlated with Secchi disk depth and inversely correlated with total phosphorus concentration. Because of its shallow depth, the effect of low reservoir levels may disproportionately affect Iola basin compared to other basins, resulting in algal blooms and toxin production especially at reservoir levels below about 7,470 feet above North American Vertical Datum of 1988. Elevated phosphorus at low reservoir level likely was primarily phosphorus contained in algal tissue. This report indicates that the main driver for recent toxic cyanoHABs in Iola basin is low reservoir level that likely causes favorable conditions (shallow and warm) for algal growth and increased recruitment of algae from bottom sediments such as during wind-driven turbulence. Control of external nutrients to the reservoir is unlikely to help control algal blooms because Aphanizomenon fixes nitrogen from the atmosphere, and there is an abundant geogenic source of phosphorus. Maintenance of reservoir levels greater than about 7,470 feet might help minimize the occurrence of toxic cyanoHABs. Additional data could help better understand how the timing and duration of reservoir levels below 7,470 feet contribute to toxic cyanoHABs.

Colorado

Nearshore bathymetric mapping along a 7-mile reach of Lake Sharpe shoreline near Lower Brule, South Dakota, 2013

Shoreline erosion rates along Lake Sharpe, a Missouri River reservoir, near the community of Lower Brule, South Dakota, were studied previously during 2011–12 by the U.S. Geological Survey, the Lower Brule Sioux Tribe, and Oglala Lakota College. The rapid shoreline retreat has caused many detrimental effects along the shoreline of Lake Sharpe, including losses of cultural sites, recreation access points, wildlife habitat, irrigated cropland, and landmass. The Lower Brule Sioux Tribe is considering options to reduce or stop erosion. One such option for consideration is the placement of discontinuous rock breakwater structures in shallow water to reduce wave action at shore. Information on the depth of water and stability characteristics of bottom material in nearshore areas of Lake Sharpe is needed by the Lower Brule Sioux Tribe to develop structural mitigation alternatives. To help address this need, a bathymetric survey of nearshore areas of Lake Sharpe near Lower Brule, South Dakota, was completed in 2013 by the U.S. Geological Survey in cooperation with the Lower Brule Sioux Tribe. HYPACK® hydrographic survey software was used to plan data collection transects for a 7-mile reach of Lake Sharpe shoreline near Lower Brule, South Dakota. Regular data collection transects and oblique transects were planned to allow for quality-assurance/quality-control comparisons. Two methods of data collection were used in the bathymetric survey: (1) measurement from a boat using bathymetric instrumentation where water was more than 2 feet deep, and (2) wading using Real-Time Kinematic Global Navigation Satellite System equipment on shore and where water was shallower than 2 feet deep. A dual frequency, 24- or 200-kilohertz narrow beam, depth transducer was used in conjunction with a Teledyne Odom CV100 dual frequency echosounder for boat-based data collection. In water too shallow for boat navigation, the elevation and nature of the reservoir bottom were mapped using Real-Time Kinematic Global Navigation Satellite System equipment. Once the data collection effort was completed, data editing was performed in HYPACK® to remove erroneous data points and to apply water-surface elevations. Maps were developed separately for water depth and bottom elevation for the study area. Lines of equal water depth for 2, 3, 3.5, 4, and 5 feet from the water surface to the lake bottom were mapped in nearshore areas of Lake Sharpe. Overall, water depths stay shallow for quite a distance from shore. In the 288 transects that crossed a 2 foot depth line, this depth occurred an average of 88 feet from shore. Similarly, in the 317 transects that crossed a 3 foot depth line, this did not occur until an average of 343 feet from shore. Elevation contours of the lake bottom were mapped primarily for elevations ranging from 1,419 to 1,416 feet above North American Vertical Datum of 1988. Horizontal errors of the Real-Time Kinematic Global Navigation Satellite System equipment for the study area are essentially inconsequential because water depth and bottom elevation were determined to change relatively slowly. The estimated vertical error associated with the Real-Time Kinematic Global Navigation Satellite System equipment for the study area ranges from 0.6 to 0.9 inch. This vertical error is small relative to the accuracy of the bathymetric data. Accuracy assessments of the data collected for this study were computed according to the National Standard for Spatial Data Accuracy. The maps showing the lines of equal water depth and elevation contours of the lake bottom are able to support a 1-foot contour interval at National Standards for Spatial Data Accuracy vertical accuracy standards, which require a vertical root mean squared error of 0.30 foot or better and a fundamental vertical accuracy calculated at the 95-percent confidence level of 0.60 foot or better.

South Dakota

Hand-hewn granite basins at Native American saltworks, Sierra Nevada, California

This site in the northern Sierra Nevada contains about 369 circular basins carved in fresh, glaciated granodioritic bedrock, with 325 basins crowded together in an area of 2,700 m 2 on the main terrace. These terrace basins have a median average diameter of 125 cm (80 percent between 100 and 160 cm) and a median depth of 75–80 cm. They show a strong congruity to similar granitic basins in the southern Sierra Nevada apparently of Native American origin that are generally shallower. The basins are not of natural origin, as indicated by uniformity in size and nonoverlapping character of the basins; their common arrangement in lineaments; details of the shape of the basins; features in common with granite basins in the Southern Sierra Nevada; and, most compelling, the clustering of all the basins adjacent to (within 20 m of) two saline streams fed from a nearby salt spring. Native Americans apparently excavated them for the purpose of collecting saline water to evaporate and make salt for their use, and also as an animal attractant and a trade commodity. The flow of the salty streams delivers about 2.9 metric tons of salt per summer season to the basin area, and evaporation rates and the holding capacity of the basins indicate that about 2.5 tons of salt could be produced per season. This correspondence shows that the Indians made enough basins to exploit the resource. The site is the most impressive prehistoric saltworks yet discovered in North America and represents a unique departure from traditional hunter-gatherer activities to that of manufacturing. The actual grinding of so many basins in granite could not have been done without the labor of a concentrated population. It is believed that the work was accomplished over a long time by many people and with the use of fire to help disaggregate the bedrock.

Scientific Investigations Report

Plant macrofossil data for 48-0 ka in the USGS North American Packrat Midden Database, version 5.0

Plant macrofossils from packrat ( Neotoma spp.) middens provide direct evidence of past vegetation changes in arid regions of North America. Here we describe the newest version (version 5.0) of the U.S. Geological Survey (USGS) North American Packrat Midden Database. The database contains published and contributed data from 3,331 midden samples collected in southwest Canada, the western United States, and northern Mexico, with samples ranging in age from 48 ka to the present. The database includes original midden-sample macrofossil counts and relative-abundance data along with a standardized relative-abundance scheme that makes it easier to compare macrofossil data across midden-sample sites. In addition to the midden-sample data, this version of the midden database includes calibrated radiocarbon ( 14 C) ages for the midden samples and plant functional type (PFT) assignments for the midden taxa. We also provide World Wildlife Fund ecoregion assignments and climate and bioclimate data for each midden-sample site location. The data are provided in tabular (.xlsx), comma-separated values (.csv), and relational database (.mdb) files.

Scientific Data

United States-Mexican Borderlands: Facing tomorrow's challenges through USGS science

Along the nearly 3,200 kilometers (almost 2,000 miles) of the United States–Mexican border, in an area known as the Borderlands, we are witnessing the expression of the challenges of the 21st century. This circular identifies several challenge themes and issues associated with life and the environment in the Borderlands, listed below. The challenges are not one-sided; they do not originate in one country only to become problems for the other. The issues and concerns of each challenge theme flow in both directions across the border, and both nations feel their effects throughout the Borderlands and beyond. The clear message is that our two nations, the United States and Mexico, face the issues in these challenge themes together, and the U.S. Geological Survey (USGS) understands it must work with its counterparts, partners, and customers in both countries. Though the mission of the USGS is not to serve as land manager, law enforcer, or code regulator, its innovation and creativity and the scientific and technical depth of its capabilities can be directly applied to monitoring the conditions of the landscape. The ability of USGS scientists to critically analyze the monitored data in search of signals and trends, whether they lead to negative or positive results, allows us to reach significant conclusions—from providing factual conclusions to decisionmakers, to estimating how much of a natural resource exists in a particular locale, to predicting how a natural hazard phenomenon will unfold, to forecasting on a scale from hours to millennia how ecosystems will behave. None of these challenge themes can be addressed strictly by one or two science disciplines; all require well-integrated, cross-discipline thinking, data collection, and analyses. The multidisciplinary science themes that have become the focus of the USGS mission parallel the major challenges in the border region between Mexico and the United States. Because of this multidisciplinary approach, the USGS possesses a unique set of capabilities that can address these challenges. The USGS can apply geographical, geospatial, biological, hydrological, and geological sciences to these complex issues and thereby provide insight into the area’s natural systems and their relation to human activity. As we come to better understand the complexities of the components of these challenge themes, we discover that each part is inextricably intertwined with other overarching issues. Because of the complex interactions of the human, ecological, political, and economic exigencies associated with this area, the status of the Borderlands has become an ever-present concern for most American citizens and for Mexican and United States Federal, State, and local governments. This circular is intended to provide you - citizen, local decisionmaker, government leader, or private entrepreneur—an overview of what the USGS considers the current and future challenges in the United States–Mexican border region and examples of how the USGS can make a difference in understanding and addressing these issues.

United States-Mexico Borderlands

Cascadia Margin cold seeps: Subduction zone fluids, gas hydrates, and chemosynthetic habitats

Priority Geographic Area: The outer continental shelf and upper continental slope from Canada/U.S. border offshore Washington State to the Mendocino Fracture Zone (Northern California), entirely within the U.S. Exclusive Economic Zone (EEZ), from the outermost shelf to at least 2000 m water depth (Figure 1). Description of Priority Area: Since 2015, over a thousand water column gas plumes originating at seafloor gas seeps have been discovered landward of the Cascadia deformation front (e.g., Embley et al., 2016; Johnson et al., 2015, 2019; Merle and Embley, 2016; NA-95 Cruise Report, 2018; Riedel et al., 2018), adding to those that had long been known on Hydrate Ridge (e.g., Heeschen et al., 2003; Tréhu et al., 2004). The recently-discovered seeps stretch from offshore Vancouver Island to the Mendocino Fracture Zone and from the outer shelf to ~2000 m water depth, occurring both landward and seaward of the nominal limit for gas hydrate stability zone on the upper continental slope (Figure 1). Hundreds of seeps likely remain undiscovered. Water column imaging is incomplete both within the target geographic area and farther seaward, between the 2000 m isobath and the deformation front, which is the subject of an imaging study described in a white paper by Watt et al. The recently-discovered Cascadia Margin cold seeps partially overlap an important active margin gas hydrate province (Spence et al., 2001; Tréhu et al., 2003, 2004), as well as an area where sediments on the North American plate are folded and faulted and affected by fluids generated in the subduction complex beneath the Cascadia forearc (e.g., Saffer and Tobin, 2011). Several Ocean Drilling Program expeditions have focused on hydrate systems offshore Vancouver and Oregon (e.g., Riedel et al., 2009; Tréhu et al., 2004) and on the connection between the shallow and deep hydrogeologic systems. Cabled observatories now continuously monitor physical, chemical, and venting processes on south Hydrate Ridge (OOI; e.g., Philip et al., 2016a) and offshore Vancouver Island (NEPTUNE; e.g. Römer et al., 2016). Outside of these well-studied gas hydrate areas, a subset of the recently-discovered Cascadia seeps, including some that we visited with R/V Falkor in 2019 (e.g., https://schmidtocean.org/cruise/methane-seeps-at-edge-of-hydrate-stability/), also likely emit methane associated with shallow subseafloor gas hydrate systems. Other seeps are delivering not only methane, but also deep-derived gases (Baumberger et al., 2018, 2020) to the seafloor. Many Cascadia Margin seeps have also been recognized at water depths too shallow (e.g., 175 m) to be connected to gas hydrate dynamics. These seeps are postulated to be emitting gas and fluids that originated deep in accretionary wedge before migrating up normal faults generated during forearc extension associated with large earthquakes (Johnson et al., 2019). Only a small fraction of the recently discovered U.S. Cascadia Margin water column gas plumes has so far been verified by ROVs (Hercules from E/V Nautilus in 2016 and 2018; SuBastian from R/V Falkor in 2018 and 2019) to correspond to seafloor seeps. Careful scientific mapping, investigation, and sampling at the seeps have also been limited (e.g., Baumberger et al., 2018, 2020; Merle and Embley, 2016; Seabrook et al., 2018; Greinert et al. 2019). This white paper focuses on expanding exploration of already-identified U.S. Cascadia Margin cold seeps through a multipronged and multidisciplinary discovery program that could be accomplished with a variety of NOAA assets. The goals of the proposed exploration activities are to develop high-resolution maps of seep fields from deep ocean vehicles; to verify (and sample) seafloor gas emissions at the locations of water column plumes for compositional and isotopic studies; to map, sample, and conduct analyses on chemosynthetic communities and deep-sea coral habitats near seep sites to document species distributions and habitats as a function of depth and latitude along the margin; to collect seep geologic samples that can constrain the timing of methane emissions through geochronology; and to record environmental data (e.g., CTD) near the seafloor and in the water column above the seeps. Seafloor mapping using shipboard systems (multibeam/backscatter) would be needed to characterize seafloor features near seep sites. Water column imaging (EK60/80 and/or multibeam WCD data) conducted before and after seafloor explorations would capture active methane plumes and constrain temporal variations in seep emissions (e.g., Kannberg et al., 2013; Philip et al., 2016a, 2016b), which are known to vary on time scales as rapid as tidal cycles on this margin (e.g., Römer et al., 2016). What are the characterization and data needs in this area? Check all that apply: __x_ Biology, Geology, Physical Oceanography, Chemistry ___ Marine Archaeology ___ Other Provide a list or brief description of the data needed within this area, from your perspective: 1. Water column backscatter to image active gas plumes 2. High-resolution multibeam bathymetry, seafloor backscatter, and shallow sub-bottom imaging 3. Visual characterization and ground truthing of potential seeps, including high-resolution mapping and photography from near-seafloor vehicles; collection of seep-associated species, corals, sediments, authigenic carbonates, gases, and seawater Describe relevance to national security, conservation, and/or the economy: The Cascadia margin seeps provide significant ecosystem services, including habitat for commercially important fishes and support for diversity along the continental margin. Methane seeps are also biological hotspots for krill, plankton, and crustaceans, which in turn sustain higher trophic levels (e.g., whales). Methane-derived authigenic carbonates serve as a hard substrate for deep-sea corals and sponges on millennial time scales. The studies proposed here will elucidate the relationship among seep environments, deep-sea corals, sponges, fisheries, and other organisms and provide new insight into subduction zone and hydrate-associated fluids in this important seismogenic zone. The studies address fishery management concerns and inform future conservation of sensitive species (e.g., deep-sea corals) and benthic habitats. From your perspective, what makes this area unique? The Cascadia Margin seeps are a critical component of the leaky margin that stretches from Baja California to the Aleutian Arc along the Pacific coastline of North America. Cold seeps have been intensely studied on the Gulf of Mexico and U.S. Atlantic passive margins with a focus on chemosynthetic communities, deep-sea corals, and leakage of microbially-generated and/or thermogenic hydrocarbons; however, the recently-discovered Cascadia Margin seeps, as well as active margin seep systems in general, remain more poorly characterized. Such seeps not only contribute to the ocean carbon cycle (e.g., Pohlman et al., 2011), thereby fueling the base of the food chain in these settings, but also emit subduction zone fluids that provide clues about processes within the seismogenic zone and the accretionary complex. The Cascadia seeps area allows both biological (e.g., benthic habitats, coral distributions) and physical processes (e.g., generation of subduction zone fluids) to be studied along both depth (perpendicular to the deformation front) and latitudinal gradients.

California, Oregon, Washington

Binning singletons: Mentoring through networking at ASM microbe 2019

The American Society for Microbiology (ASM) national conference, Microbe, is the flagship meeting for microbiologists across the globe. The presence of roughly 10,000 attendees provides enormous opportunities for networking and learning. However, such a large meeting can be intimidating to many, especially early career scientists, students, those attending alone, and those from historically underrepresented groups. While mentorship is widely valued by ASM and its members, finding concrete ways to develop new and diverse mentoring opportunities can be a challenge. We recognized the need for an initiative aimed at expanding peer-to-peer mentoring, facilitating networking, and providing support for Microbe attendees; therefore, we created the program Binning Singletons for ASM Microbe 2019. The program consisted of five steps named after tools or phenomena in the profession of microbiology: (i) Identify the Singletons (e.g., individuals attending alone), (ii) Bin the Singletons, (iii) Horizontal Transfer, (iv) Quorum Sensing, and (v) Exponential Growth. These steps resulted in the matching of participants unsure of how to get the most out of their conference experience (e.g., singletons) with mentors who assisted with meeting planning, networking, and/or impostor syndrome. Started on social media only a month before ASM Microbe 2019, the program successfully launched despite limited time and resources. Binning Singletons improved inclusivity and networking opportunities for participants at the conference. Here, we discuss what worked, and what can be improved, with an eye toward development of the Binning Singletons model for future conferences to provide opportunities to increase inclusivity, networking, and accessibility for singletons and build a stronger scientific community.

mSphere

Heterogeneity of a landscape influences size of home range in a North American cervid

In the northeastern United States, chronic wasting disease has recently been detected in white-tailed deer ( Odocoileus virginianus ) populations, and understanding the relationship between landscape configuration and home range may improve disease surveillance and containment efforts. The objectives of our study were to compare size of home range for deer occupying a continuum of forested landscapes and to investigate relationships between size of home range and measures of landscape configuration. We used a movement-based kernel density estimator to estimate home range at five spatial scales among deer across study areas. We developed 7 linear regression models that used measures of the configuration of the forested landscape to explain size of home range. We observed differences in size of home range between sexes among areas that differed based on landscape configuration. We documented size of home range changed with various metrics that identifying connectivity of forested patches. Generally, size of home range increased with an increasing proportion of homogenous forest. Our results suggest that deer in our region occupy a landscape at hierarchically-nested scales that is controlled by the connectivity of the forested landscape across local or broad geographical regions.

Pennsylvania

Flood-inundation maps for the Saddle River from Rochelle Park to Lodi, New Jersey, 2012

Digital flood-inundation maps for a 2.75-mile reach of the Saddle River from 0.2 mile upstream from the Interstate 80 bridge in Rochelle Park to 1.5 miles downstream from the U.S. Route 46 bridge in Lodi, New Jersey, were created by the U.S. Geological Survey (USGS) in cooperation with the New Jersey Department of Environmental Protection (NJDEP). The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation , depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage at Saddle River at Lodi, New Jersey (station 01391500). Current conditions for estimating near real-time areas of inundation using USGS streamgage information may be obtained on the Internet at http://waterdata.usgs.gov/nwis/uv?site_no=01391500 . The National Weather Service (NWS) forecasts flood hydrographs at many places that are often collocated with USGS streamgages. NWS-forecasted peak-stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. In this study, flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. The model was calibrated using the most current stage-discharge relations at the Saddle River at Lodi, New Jersey streamgage and documented high-water marks from recent floods. The hydraulic model was then used to determine 11 water-surface profiles for flood stages at the Saddle River streamgage at 1-ft intervals referenced to the streamgage datum, North American Vertical Datum of 1988 (NAVD 88), and ranging from bankfull, 0.5 ft below NWS Action Stage, to the extent of the stage-discharge rating, which is approximately 1 ft higher than the highest recorded water level at the streamgage. Action Stage is the stage which when reached by a rising stream the NWS or a partner needs to take some type of mitigation action in preparation for possible significant hydrologic activity. The simulated water-surface profiles were then combined with a geographic information system 3-meter (9.84-ft) digital elevation model (derived from Light Detection and Ranging (LiDAR) data) in order to delineate the area flooded at each water level. The availability of these maps, along with Internet information regarding current stage from USGS streamgages and forecasted stream stages from the NWS, provide emergency management personnel and residents with information that is critical for flood response activities, such as evacuations and road closures, as well as for post-flood recovery efforts.

New Jersey

Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse

The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse ( Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.

Scientific Reports

Data and knowledge gaps of a water bottling facility inventory and select water-use dataset, United States

In 2023, the U.S. Geological Survey developed a national inventory of water bottling facilities for the United States, including information about locations, water sources, water use, and a collection of other attributes. The purpose of the inventory was to provide information about water bottling facilities needed to assess and improve understanding of local-, regional-, and national-scale hydrologic and socioeconomic effects resulting from water extraction for bottling. Beverage types coded in the North American Industry Classification System under subsector 312 (Beverage and Tobacco Product Manufacturing) were compiled; however, facility information was often not publicly available, time intensive to search manually, and difficult to verify because there are no nationally available facility lists. A separate evaluation of facilities in the Great Lakes region identified some facilities that were missing and some with incorrect information. Ancillary facility attributes were primarily available from a proprietary business dataset and water-use data could only be acquired for a small subset of facilities. These limitations and deficiencies may affect the types of analyses that can be done using the inventory information. Therefore, the following data-quality aspects are used to describe the information compiled in the facility and water-use tables: completeness, uniqueness, validity, timeliness, accuracy, consistency, and accessibility. The resulting implications of the data and knowledge gaps are that users of the data may need to make additional evaluations of the inventory information for some analyses.

Scientific Investigations Report

Flood-inundation maps for the Saddle River from Upper Saddle River Borough to Saddle River Borough, New Jersey, 2013

Digital flood-inundation maps for a 4.1-mile reach of the Saddle River from 0.6 miles downstream from the New Jersey-New York State boundary in Upper Saddle River Borough to 0.2 miles downstream from the East Allendale Road bridge in Saddle River Borough, New Jersey, were created by the U.S. Geological Survey (USGS) in cooperation with the New Jersey Department of Environmental Protection (NJDEP). The inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science Web site at http://water.usgs.gov/osw/flood_inundation/, depict estimates of the areal extent and depth of flooding corresponding to select water levels (stages) at the USGS streamgage 01390450, Saddle River at Upper Saddle River, New Jersey. Current conditions for estimating near real-time areas of inundation using USGS streamgage information may be obtained on the Internet at http://waterdata.usgs.gov/nwis/uv?site_no=01390450. The National Weather Service (NWS) forecasts flood hydrographs at many places that are often collocated with USGS streamgages. NWS-forecasted peak-stage information may be used in conjunction with the maps developed in this study to show predicted areas of flood inundation. In this study, flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. The model was calibrated by using the most current stage-discharge relations (in effect March 2013) at USGS streamgage 01390450, Saddle River at Upper Saddle River, New Jersey, and documented high-water marks from recent floods. The hydraulic model was then used to determine eight water-surface profiles for flood stages at 0.5-foot (ft) intervals referenced to the streamgage datum, North American Vertical Datum of 1988 (NAVD 88), and ranging from bankfull, 0.5 ft below NWS Action Stage, to the upper extent of the stage-discharge rating which is approximately 1 ft higher than the highest recorded water level at the streamgage. Action Stage is the stage which when reached by a rising stream the NWS or a partner needs to take some type of mitigation action in preparation for possible significant hydrologic activity. The simulated water-surface profiles were then combined with a geographic information system 3-meter (9.84 ft) digital elevation model (derived from Light Detection and Ranging (LiDAR) data) in order to delineate the area flooded at each water level. The availability of these maps along with real-time streamflow data and information regarding current stage from USGS streamgages and forecasted stream stages from the NWS provide emergency management personnel and residents with information that is critical for flood response activities, such as evacuations and road closures, as well as for post-flood recovery efforts.

New Jersey

Making Recursive Bayesian inference accessible

Bayesian models provide recursive inference naturally because they can formally reconcile new data and existing scientific information. However, popular use of Bayesian methods often avoids priors that are based on exact posterior distributions resulting from former studies. Two existing Recursive Bayesian methods are: Prior- and Proposal-Recursive Bayes. Prior-Recursive Bayes uses Bayesian updating, fitting models to partitions of data sequentially, and provides a way to accommodate new data as they become available using the posterior from the previous stage as the prior in the new stage based on the latest data. ProposalRecursive Bayes is intended for use with hierarchical Bayesian models and uses a set of transient priors in first stage independent analyses of the data partitions. The second stage of Proposal-Recursive Bayes uses the posteriors from the first stage as proposals in an MCMC algorithm to fit the full model. We combine Prior- and Proposal-Recursive concepts to fit any Bayesian model, and often with computational improvements. We demonstrate our method with two case studies. Our approach has implications for big data, streaming data, and optimal adaptive design situations.

American Statistician

Storage capacity and sedimentation characteristics of the San Antonio Reservoir, California, 2018

The San Antonio Reservoir is a large water storage facility in Alameda County, California, and is a major component of the Hetch Hetchy Regional Water System (RWS). The RWS is a water-supply system owned and operated by the San Francisco Public Utilities Commission (SFPUC) and provides water for about 2.7 million people in the San Francisco, Santa Clara, Alameda, and San Mateo Counties. The San Antonio Reservoir is one of two RWS reservoirs in Alameda County and the third largest of the RWS reservoirs in the San Francisco Bay Area. The reservoir was formed by the James H. Turner Dam, which was completed in 1965. At the time of construction, the reservoir was estimated to have 50,500 acre-feet (acre-ft) of storage capacity. That early estimate was based on a 1963 pre-construction topographic map, which was drawn from aerial photographs. The capacity of the reservoir was later surveyed in 1994 and 2000. These two later surveys did not include the upper 18 feet (ft) of the reservoir, which represents roughly 30 percent of the overall storage volume. To determine the storage capacity and provide updated stage-capacity curves up to the spillway, the U.S. Geological Survey, in cooperation with the SFPUC, surveyed the bathymetry and shoreline of the reservoir in April 2018. The bathymetric survey was performed by making depth soundings using a boat-mounted, multibeam echosounder. At the time of the survey, the water level was between 13 and 14 ft below the spillway elevation. To measure capacity between the water line up to the spillway elevation, topography along most of the shoreline was surveyed from the boat using a terrestrial Light Detection and Ranging (LiDAR) scanner and in other areas by using ground-survey techniques. Location during bathymetric and topographic data collection was determined using a Global Navigation Satellite System-Real Time Network system. Vertical profiles of sound speed were collected periodically. The sound-speed profiles were used to spatially and temporally adjust the sound-speed calculations used to determine depth from the soundings. Approximately 125 kilometers (78 miles) of transects with a total of about 560 million depth soundings and topographic LiDAR points were collected (about 160 per square meter). In addition, approximately 500 topographic survey points were collected in shallow, wadable areas and on land near the upper reservoir area using a Global Navigation Satellite System receiver attached to a fixed length survey rod. Depth soundings, terrestrial LiDAR points, topographic survey points, and a digitized shoreline were merged and interpolated to generate a digital elevation model (DEM) of the reservoir. Gridded elevation data extracted from the DEM were then tabulated to determine total reservoir capacity and create reservoir stage-surface area and stage-storage capacity tables. Results of the reservoir capacity analysis indicated that the reservoir has 53,266 (plus or minus 140) acre-ft of storage capacity, which is an increase of 2,766 acre-ft (or 5.5 percent) greater than the original 1965 estimate; the increase is likely due to improved survey methods. Also, at the time of this 2018 survey, Intake #1 (the lowest intake) was not in operation. Intake #1 is estimated to be buried approximately 10 ft below the bed, whereas Intake #2 is about 20 ft above the bed. There are five intakes at different elevation levels; however, when consecutive lower intakes become inoperable due to sedimentation, the live storage capacity (capacity available for use) is reduced. At the time of this survey, the remaining live storage (above Intake #2) was approximately 52,363 acre-ft. The 2018 stage-capacity curve was compared to the original 1965 stage-capacity curve. Although overall, the changes indicate an increase in storage capacity, the change in volume at 372.7 ft North American Vertical Datum of 1988 (370 ft National Geodetic Vertical Datum of 1929, NGVD 29) shows a decrease of 733 acre-ft (the elevation of 370 ft NGVD 29 was used because it is the lowest elevation available for the 1965 stage-capacity curves). This finding agrees with the observed accumulation of sediment over Intake #1. That volume was converted to an annual sediment yield of 0.35 acre-ft per square mile (or 165 cubic meters per square kilometer), which is of the same order of magnitude as that found in other watersheds for the Coast Ranges in California. A decrease of 733 acre-ft between 1965 and 2018 thus represents a loss of 1.5 percent of the overall storage capacity in the reservoir. The updated stage-surface area and stage-capacity tables provided in this report and online ( https://doi.org/10.5066/P9KC9DU8 ) can be used by the SFPUC to improve reservoir operations and serve as an accurate baseline to monitor bathymetric changes in the future.

California