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Publications recently added to the Pubs Warehouse

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Biological assessment of a proposed vegetation management program to benefit Tribes in eastern Oklahoma

Released July 02, 2020 16:30 EST

2020, Open-File Report 2020-1013

Benjamin R. Harms, Heidi L. Bencin, Natasha B. Carr

Tribal communities may benefit from land management activities that enhance their use of resources on tribal lands. The Bureau of Indian Affairs is implementing a 5-year vegetation management program to provide support for projects that develop and use natural and cultural resources and improve opportunities for agricultural activities to benefit 20 Indian Tribes and Nations in the Eastern Oklahoma Region of the Bureau of Indian Affairs. The bureau is working with individual Tribes to identify project objectives and design treatments, which include prescribed burning, timber removal, thinning, and reduction of hazardous fuels. The total action area for the vegetation management program is estimated to be 236,575 acres, representing approximately 1 percent of the region.

A biological assessment was prepared, in cooperation with the bureau and U.S. Fish and Wildlife Service, to evaluate the potential effects of the proposed vegetation management program on 22 federally threatened, endangered, and candidate species that may occur within the Eastern Oklahoma Region. The species evaluated included one plant, two insects, one reptile, five fresh-water mussels, four fishes, five birds, and four bats. Because the proposed treatments will be largely restricted to terrestrial systems, it is expected that there will be no adverse effects on the 15 species associated with aquatic habitats, provided that best management practices are followed. The proposed treatments may affect but are unlikely to adversely affect six of the primarily terrestrial species (the Papaipema eryngii [rattlesnake master borer], Picoides borealis [red-cockaded woodpecker], Myotis grisescens [gray bat], Myotis sodalis [Indiana bat], Myotis septentrionalis [northern long-eared bat], and Corynorhinus townsendii ingens [Ozark big-eared bat]), provided that best management practices are followed, including avoidance of critical habitat features.

The only species likely to be adversely affected by the proposed treatments is Nicrophorus americanus (American burying beetle) as a consequence of short-term disturbances to soils and vegetation. Most adverse effects of the treatments (such as soil compaction and decreased cover in the forest understory) are expected to be short term (habitat will recover or be restored within 5 years of treatments). Less than 1 percent of the action area is expected to result in long-term adverse effects to the American burying beetle as a result of permanent cover changes that persist for more than 5 years. It is expected that the primary treatments will be largely beneficial to the American burying beetle population in the region by reducing the risk of high-severity fires and expansion of invasive woody shrubs, such as Juniperus virginiana (eastern redcedar) within potential beetle habitat and the surrounding landscape. Overall, the proposed management program is expected to provide long-term benefits to American burying beetle habitat across 91 percent of the action area.

In situ observations of wave transformation and infragravity bore development across reef flats of varying geomorphology

Released July 02, 2020 15:27 EST

2020, Frontiers in Marine Science (7)

Olivia Cheriton, Curt D. Storlazzi, Kurt J. Rosenberger

The character and energetics of infragravity (IG, 25 s < period < 250 s) and very-low frequency (VLF, period > 250 s) waves over coral reef flats can enhance shoreline erosion or accretion, and also govern extreme shoreline events such as runup, overwash, and flooding on coral reef-lined coasts. Here we use in situ wave measurements collected along cross-reef transects at 7 sites on Pacific islands with varying reef geomorphologies to examine under what conditions IG waves occur and what factors enhance their irregularity. In general, a greater fraction of total wave energy was transferred to the IG band on reefs with steeper fore reef slopes and shallower reef flats. The IG wave amplitudes scaled with increasing water levels, but it was primarily at lower water levels when these waves became pitched onshore (negatively asymmetrical) and peaked (positively skewed). However, our results also highlight the importance of reef-flat width and slope as important morphological controls on IG waves, as the most asymmetric, bore-like, IG waves occurred on the wider reef flats, and the most skewed IG waves at the site with the steepest reef-flat. On the wider reef flats, IG wave-wave capture was observed during periods of large offshore wave forcing and enhanced VLF wave energy. Because similar IG wave motions over plane beaches enhance sea-swell (SS, period < 25 s) bore-merging in the surf zone, we posit that VLF waves over reef flats may facilitate IG bore merging, and this may lead to larger, more pitched-onshore bores at the shoreline. In addition, greater IG wave heights appear to support the transmission of larger secondary short-period waves over the reef flat, independent of overall water levels. As irregular IG waves may be strong drivers of cross-reef sediment transport as well as runup, understanding the conditions and reef geomorphologies that lead to low-frequency, energetic bores on reef flats is critical to forecasting how coral reef-lined coasts will respond to sea-level rise and climate change.

Selective sediment transport during Hurricane Sandy on Fire Island (New York, USA): Inferences from heavy-mineral assemblages

Released July 02, 2020 15:15 EST

2020, Journal of Sedimentary Research (90) 269-285

João Cascalho, Pedro Costa, Guy R. Gelfenbaum, Seanpaul La Selle, Bruce E. Jaffe

In October 2012, Hurricane Sandy caused severe erosion on beaches and dunes of Fire Island (New York, USA). Major shoreline changes occurred with erosional dominance in the upper shoreline and aggradation in the lowermost section of the beach due to the deposition of eroded upper beach and dune sediment. Sand laminations with a high concentration of heavy minerals (“black sand laminations”) were observed in three excavated trenches located on a washover terrace and fan on the east side of Fire Island. The mineralogical composition of these laminations reveals the presence of high quantities of magnetite, ilmenite (as opaque minerals), and garnet (as main translucent mineral). These heavy mineral enriched laminations were formed as waves eroded and transported sand from the primary dune and smaller relict dunes under specific hydrodynamic conditions that promoted grain sorting according to differences in size and specific gravity. Based on the concentrations of certain heavy minerals, the threshold for primarily density-driven sorting probably lies between the specific gravity of a less dense mineral (ilmenite, 4.7) and Garnet almandine (4.3), the most common transparent heavy mineral. The number of laminations and concentrations of heavy minerals vary between trenches on the overwash terrace and appear to be controlled by their distance from sediment sources. The trench with a greatest number of laminations and higher heavy mineral concentrations is located furthest from the main dune but is just 10 m inland of a relict dune that acts as the primary source of sediment of the washover deposit in this trench. A conceptual model for heavy mineral layer deposition is presented based on geomorphological and sedimentological evidences allowing the definition of a density threshold.

When and where: estimating the date and location of introduction for exotic pests and pathogens

Released July 02, 2020 14:16 EST

2020, Article

Trevor J. Hefley, Robin E. Russell, Anne Ballmann, Haoyu Zhang

1. A fundamental question during the outbreak of a novel disease or invasion of an exotic pest is: At what location and date was it first introduced? With this information, future introductions can be anticipated and perhaps avoided. 2. Point process models are commonly used for mapping species distribution and disease occurrence. If the time and location of introductions were known, then point process models could be used to map and understand the factors that influence introductions, however, rarely is the process of introduction directly observed. 3. We propose embedding a point process within hierarchical Bayesian models commonly used to understand the spatio-temporal dynamics of invasion. Including a point process within a hierarchical Bayesian model enables inference regarding the location and date of introduction from indirect observation of the process such as species or disease occurrence records. We illustrate our approach using disease surveillance data collected to monitor white-nose syndrome, which is a fungal disease that threatens many North American species of bats. We use our model and surveillance data to estimate the location and date that the pathogen was introduced into the United States. Finally, we compare forecasts from our model to forecasts obtained from state-of-the-art regression-based statistical and machine learning methods. 4. The pathogen that causes white-nose syndrome was most likely introduced into the United States four years prior to the first detection, but there is a moderate level of uncertainty in this estimate. Our results show that the location of introduction could be up to 510 km east of the location of first discovery, but our results also suggest that there is a relatively high probability the location of first detection could be the location of introduction.

Toxicity and bioavailability of metals in the Missouri River adjacent to a lead refinery

Released July 02, 2020 13:30 EST

2001, Biological Science Report 2001-0004

Duane C. Chapman, Ann L. Allert, James F. Fairchild, Thomas W. May, Christopher J. Schmitt, Edward V. Callahan

This study is an evaluation of the potential environmental impacts of contaminated groundwater from the ASARCO metals refining facility adjacent to the Missouri River in Omaha, Nebraska. Surface waters, sediments, and sediment pore waters were collected from the Burt-Izard drain, which transects the facility, and from the Missouri River adjacent to the facility. Groundwater was also collected from the facility. Waters and sediments were analyzed for inorganic contaminants, and the toxicity of the waters was evaluated with the Ceriodaphnia dubia 7-day test. Concentrations of several elemental contaminants were highly elevated in the groundwater, but not in river sediment pore waters. Lead concentrations were moderately elevated in whole sediment at one site, but lead concentrations in pore waters were low due to apparent sequestration by acid-volatile sulfides. The groundwater sample was highly toxic to C. dubia, causing 100% mortality. Even at the lowest groundwater concentration tested (6.25%) C. dubia survival was reduced; however, at that concentration, reproduction was not significantly different from upstream porewater reference samples. Sediment pore waters were not toxic, except reproduction in pore water collected from one downstream site was somewhat reduced. The decrease in reproduction could not be attributed to measured elemental contaminants.

Initial biotic survey of Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge

Released July 02, 2020 13:30 EST

1999, Biological Science Report 2000-0001

Dale D. Humburg, Vincent J. Burke

The 2,300-acre Lisbon Bottom Unit, located in central Missouri, became part of the Big Muddy National Fish and Wildlife Refuge (NFWR) after the Great Flood of 1993 devastated the Unit's farmland and network of levees. As a result, interdisciplinary studies were initiated through collaboration among various researches, universities, and State and Federal conservation agencies to investigate the short-term effects of the flood and to expand information about the Missouri River and flood-plain systems. The studies included in these chapters investigate diverse aspects of Lisbon Bottom Unit's physical setting and biota and provide baseline information that managers can use to assess restoration efforts on Lisbon Bottom and other units of the Big Muddy NFWR.

Space use and relative habitat selection for immature green turtles within a Caribbean marine protected area

Released July 02, 2020 13:22 EST

2020, Animal Biotelemetry (8)

Lucas P Griffin, Brian J. Smith, Michael Cherkiss, Andrew Crowder, Clayton G Pollock, Zandy Hillis-Starr, Andy J. Danylchuk, Kristen Hart

Background A better understanding of sea turtle spatial ecology is critical for the continued conservation of imperiled sea turtles and their habitats. For resource managers to develop the most effective conservation strategies, it is especially important to examine how turtles use and select for habitats within their developmental foraging grounds. Here, we examine the space use and relative habitat selection of immature green turtles (Chelonia mydas) using acoustic telemetry within the marine protected area, Buck Island Reef National Monument (BIRNM), St. Croix, United States Virgin Islands. Results Space use by turtles was concentrated on the southern side of Buck Island, but also extended to the northeast and northwest areas of the island, as indicated by minimum convex polygons (MCPs) and 99%, 95%, and 50% kernel density estimations (KDEs). On average space use for all categories was<3 km2 with mean KDE area overlap ranging from 41.9 to 67.7%. Cumulative monthly MCPs and their proportions to full MCPs began to stabilize 3 to 6 detection months after release, respectively. Resource selection functions (RSFs) were implemented using a generalized linear mixed effects model with turtle ID as the random effect. After model selection, the accuracy of the top model was 77.3% and showed relative habitat selection values were highest at shallow depths, for areas in close proximity to seagrass, and in reef zones for both day and night, and within lagoon zones at night. The top model was also extended to predict across BIRNM at both day and night. Conclusion More traditional acoustic telemetry analyses in combination with RSFs provide novel insights into animal space use and relative resource selection. Here, we demonstrated immature green turtles within the BIRNM have small, specific home ranges and core use areas with temporally varying relative selection strengths across habitat types. We conclude the BIRNM marine protected area is providing sufficient protection for immature green turtles, however, habitat protection could be focused in both areas of high space use and in locations where high relative selection values were determined. Ultimately, the methodologies and results presented here may help to design strategies to expand habitat protection for immature green turtles across their greater distribution.

Biology of the Rio Grande border region : A bibliography

Released July 02, 2020 13:10 EST

1997, Information and Technology Report 1997-0001

Lynne E. Johnson, Linda J. Jacobs, Diana Papoulias

This bibliography includes 1,913 references to the literature of the Rio Grande (Rio Bravo del Norte). The specific geographic area covered extends 100 km on either side of the river from Elephant Butte Dam in New Mexico to the Gulf of Mexico. The bibliography focuses on the biological literature, divided into major subject areas, and also includes supporting literature from the physical and environmental sciences.

Prioritizing river basins for intensive monitoring and assessment by the US Geological Survey

Released July 02, 2020 13:07 EST

2020, Environmental Modeling & Assessment (192)

Peter C. Van Metre, Sharon L. Qi, Jeffrey R. Deacon, Cheryl A. Dieter, Jessica M. Driscoll, Michael N. Fienen, Terry A. Kenney, Patrick M. Lambert, David Paul Lesmes, Christopher Allen Mason, Anke Mueller-Solger, MaryLynn Musgrove, Jaime A. Painter, Donald O. Rosenberry, Lori A. Sprague, Anthony J. Tesoriero, Lisamarie Windham-Myers, David M. Wolock

The US Geological Survey (USGS) is currently (2020) integrating its water science programs to better address the nation’s greatest water resource challenges now and into the future. This integration will rely, in part, on data from 10 or more intensively monitored river basins from across the USA. A team of USGS scientists was convened to develop a systematic, quantitative approach to prioritize candidate basins for this monitoring investment to ensure that, as a group, the 10 basins will support the assessment and forecasting objectives of the major USGS water science programs. Candidate basins were the level-4 hydrologic units (HUC04) with some of the smaller HUC04s being combined; median candidate-basin area is 46,600 km2. Candidate basins for the contiguous United States (CONUS) were grouped into 18 hydrologic regions. Ten geospatial variables representing land use, climate change, water use, water-balance components, streamflow alteration, fire risk, and ecosystem sensitivity were selected to rank candidate basins within each of the 18 hydrologic regions. The two highest ranking candidate basins in each of the 18 regions were identified as finalists for selection as “Integrated Water Science Basins”; final selection will consider input from a variety of stakeholders. The regional framework, with only one basin selected per region, ensures that as a group, the basins represent the range in major drivers of the hydrologic cycle. Ranking within each region, primarily based on anthropogenic stressors of water resources, ensures that settings representing important water-resource challenges for the nation will be studied.

Urban stream syndrome and contaminant uptake in salamanders of Central Texas

Released July 02, 2020 12:43 EST

2020, Journal of Fish and Wildlife Management (11) 287-299

Peter H. Diaz, Erik L. Orsak, Floyd W. Weckerly, Mike A. Montagne, David Alvarez

We studied the ecological health of springs experiencing varying levels of urban development to assess impacts to rare endemic salamanders (Eurycea spp.) of Central Texas. We evaluated measures of invertebrate species richness, water quality, and contaminant uptake by salamanders to determine how springs and their inhabitants were being affected by urban growth and changing land-use patterns. The number of environmental contaminants present and concentrations of contaminants increased in both water and salamander tissues with increasing age of the developments (i.e., years postconstruction) and increasing levels of impervious cover (e.g., roads) in urban watersheds compared with nondeveloped sites. We conclude that urbanization and associated increases in pollutant loading in watersheds can result in a loss of spring biodiversity and the accumulation of persistent and potentially toxic pollutants in salamanders. Although we detected generally low levels of pollutants, the altered water quality and invertebrate composition observed at springs, coupled with the changing hydrology and chronic contaminant exposure inherent in urban landscapes, is cause for concern, with potential implications for the long-term health, survival, and recovery of salamanders.

Climate-change refugia in boreal North America: What, where, and for how long?

Released July 02, 2020 11:38 EST

2020, Frontiers in Ecology and the Environment (18) 261-270

Diana Stralberg, Dominique Arseneault, Jennifer Baltzer, Quinn Barber, Erin Bayne, Yan Boulanger, Carissa Brown, Hilary Cooke, Kevin Devito, Jason Edwards, Cesar Estevo, Nadele Flynn, Lee Frelich, E. H. (T.) Hogg, Mark Johnston, Travis Logan, Steven M. Matsuoka, Paul Moore, Toni Lyn Morelli, Julienne Morissette, Elizabeth Nelson, Hedvig Nenzén, Scott Nielsen, Marc-André Parisien, John Pedlar, David Price, Fiona Schmiegelow, Stuart Slattery, Oliver Sonnentag, Daniel Thompson, Ellen Whitman

TThe vast boreal biome plays an important role in the global carbon cycle but is experiencing particularly rapid climate warming, threatening the integrity of valued ecosystems and their component species. We developed a framework and taxonomy to identify climate‐change refugia potential in the North American boreal region, summarizing current knowledge regarding mechanisms, geographic distribution, and landscape indicators. While “terrain‐mediated” refugia will mostly be limited to coastal and mountain regions, the ecological inertia (resistance to external fluctuations) contained in some boreal ecosystems may provide more extensive buffering against climate change, resulting in “ecosystem‐protected” refugia. A notable example is boreal peatlands, which can retain high surface soil moisture and water tables even in the face of drought. Refugia from wildfire are also especially important in the boreal region, which is characterized by active disturbance regimes. Our framework will help identify areas of high refugia potential, and inform ecosystem management and conservation planning in light of climate change.

Biomonitoring of Environmental Status and Trends (BEST) Program: Field procedures for assessing the exposure of fish to environmental contaminants

Released July 02, 2020 10:00 EST

1999, Information and Technology Report 1999-0007

Christopher J. Schmitt, Vicki S. Blazer, Gail M. Dethloff, Donald E. Tillitt, Timothy S. Gross, Wade L. Bryant Jr., L. Rod DeWeese, Ronald W. Goede, Timothy M. Bartish, Timothy J. Kubiak

This document describes procedures used to collect information, tissues, and fluids for documenting the exposure of fish to environmental contaminants. For the procedures described here, fish are captured (preferably by electrofishing) and held alive until processing (genearlly <1 h). Fish are weighed, measured, and examined for grossly visible external lesions and pathologies. A blood sample is collected by caudal veinipuncture using a needle and syringe. The fish is subdued, and its abdominal cavity is opened. The internal organs are dissected from the fish for examination. The sex of the fish is determined by direct observation of its gonads. The liver is weighed (most species) and cut into small cubes and flash-frozen in cryogenic vials, which are stored and shipped in dry ice or liquid nitrogen. Additional liver cubes plus all grossly visible anomalies are preserved for histopathology. The gonads and spleen are weighed, and samples are preserved for histopathology. The kidneys are examined, and histopathology samples collected. A gill sample is also collected and preserved. All remaining tissues are returned to the carcass, which is wrapped in foil, labeled for chemical analysis, and chilled. Individual fish carcasses are composited by station, species, and gender; frozen; and shipped to the analytical laboratory. Procedures are also described for record keeping; processing blood to obtain serum and plasma; flash-freezing samples; cleaning equipment; and preventing the transport of living organisms among waterways. A list of necessary equipment and supplies is also provided.

Biomonitoring of Environmental Status and Trends (BEST) Program: Selected methods for monitoring chemical contaminants and their effects in aquatic ecosystems

Released July 02, 2020 09:05 EST

2000, Information and Technology Report 2000-0005

Vicki S. Blazer, Nancy D. Denslow, Gail M. Dethloff, Timothy S. Gross, Kelly K. McDonald, Christopher J. Schmitt, Donald E. Tillitt, Jeffrey J. Whyte

Christopher J. Schmitt, Gail M. Dethloff, editor(s)

This document describes the suite of biological methods of the U.S. Geological Survey- Biomonitoring of Environmental Status and Trends program for monitoring chemical contaminants and their effects on fish. The methods, which were selected by panels of experts, are being field-tested in rivers of the Mississippi River, Columbia River, and Rio Grande basins. General health biomarkers include a health assessment index based on gross observation; histopathological examination of selected organs and tissues; condition factor; and the heptosomatic and splenosomatic indices. Immune system indicators are plasma lysozyme activity and measures of splenic macrophage aggregates. Reproductive biomarkers include plasma concentrations of sex steroid hormones (17β-estradiol and 11-ketotestosterone) and vitellogenin, gonadal histopathology (including reproductive stage and, in females, gonadal atresia), and the gonadosomatic index. Indicators of exposure to polycyclic aromatic and polyhalogenated hydrocarbons are the H4IIE rat hepatoma cell bioassay (performed on solvent extracts of composite fish samples) and hepatic ethoxyresorufin-O-deethylase activity. Stable nitrogen isotope ratios are used to assess the trophic position of the fish and their exposure to sewage and other animal wastes. For each indicator we describe endpoint(s) and methods, and discuss the indicator?s value and limitations for contaminant monitoring and assessment.

Illustrated field guide for assessing external and internal anomalies in fish

Released July 02, 2020 08:20 EST

2002, Information and Technology Report 2002-0007

Stephen B. Smith, Anne P. Donahue, Robin J. Lipkin, Vicki Blazer, Christopher J. Schmitt, Ronald W. Goede

Procedures are described for processing fish for examination of external and internal anomalies and pathologies indicative of exposure to environmental contaminants and other peturbations. For the procedures described here, fish are captured (preferably by electrofishing) and held alive until processing (generally < 1 h). Fish are weighed, measured, and necropsied, and a scale sample is obtained from for age determination. Information is given for the collection and preservation of tissue samples for histopathological analysis. Photographs of most abnormalities are included along with normal conditions for easier identification of external (oral, head, eye, gill, opercula, and fin) and internal (liver, spleen, gonad, and kidney) anomalies. The report also includes recommendations for record keeping, sample labeling, and shipping records, equipment, supplies,and samples. A list of suggested equipment and supplies for field processing is included as are instructions for cleaning equipment.

Aquatic synthesis for Voyageurs National Park

Released July 01, 2020 16:30 EST

2003, Information and Technology Report 2003-0001

Larry A. Kallemeyn, Kerry L. Holmberg, Jim A. Perry, Beth Y. Odde

Voyageurs National Park (VOYA), which was established in 1975, contains significant aquatic resources with about 50% of its total area of 883 km2 (341 mi2) consisting of aquatic habitats.  In addition to the Park's 30 named lakes, there are numerous wetlands including hundreds of beaver ponds.  Due to the Park's size and location in the drainage basin, aquatic resources within the Park are particularly susceptible to activities and developments that occur outside its' boundary.  This is particularly true in regard to the water quality and aquatic communities in the four large lakes that comprise 96% of the Park's total lake area of 34,400 ha (133 mi2).  Because most Park activities center on the lakes, particularly the large lakes, resource managers need to have knowledge and understanding of VOYA's aquatic resources to effectively preserve, in an unimpaired condition, the ecological processed, biological and cultural diversity, and history of the northwoods, lakecountry border shared with Canada.

Habitat assessment, Missouri River at Hermann, Missouri

Released July 01, 2020 16:20 EST

2002, Open-File Report 2002-32

Robert B. Jacobson, Mark S. Laustrup, Joanna M. Reuter

This report documents methods and results of aquatic habitat assessment in the Missouri River near Hermann, Missouri. The assessment is intended to improve understanding of spatial and temporal variability of aquatic habitat, including habitats thought to be critical for the endangered pallid sturgeon (Scaphirhynchus albus). Physical aquatic habitat – depth, velocity, and substrate – was assessed around 9 wing dikes and adjacent to the U.S. Route 19 bridge, at discharges varying from 44,000 cubic feet per second (cfs) to 146, 000 cfs during August 2000 – May, 2001. For the river as a whole, velocities are bi-modally distributed with distinct peaks relating to navigation channel and wing-dike environments. Velocities predictably showed an increasing trend with increasing discharge. Substrate within wing dikes was dominated by mud at low discharges, whereas the navigation channel had patches of transporting sand, rippled sand, and coarse sand. Discharges that overtopped the wing dikes (about 93,000 cfs, March 2001) were associated with increases of patchy sand, rippled sand, and coarse sand within the wing dikes. When flows were substantially over the wing dikes (146,000 cfs, May 2001) substrates within most wing dikes showed substantial reorganization and coarsening.

The habitat assessment provides a geospatial database that can be used to query wing dikes for distributions of depth, velocity, and substrate for comparison with fish samples collected by US Fish and Wildlife Service biologists (Grady and others, 2001). In addition, the assessment documented spatial and temporal variation in habitat within the Hermann reach and over a range of discharges. Measurable geomorphic change – alteration of substrate conditions plus substantial erosion and deposition – was associated with flows equaled or exceeded 12–40% of the time (40–140 days per year). Documented geomorphic change associated with high-frequency flows underscores the natural temporal variability of physical habitat in the Lower Missouri River.

Ecological dynamics of wetlands at Lisbon Bottom, Big Muddy National Fish and Wildlife Refuge, Missouri

Released July 01, 2020 15:40 EST

2002, Open-File Report 2004-1036

Duane C. Chapman, Ellen A. Ehrhardt, James F. Fairchild, Robert B. Jacobson, Barry C. Poulton, Linda C. Sappington, Brian P. Kelly, William R. Mabee

The study documented the interaction between hydrology and the biological dynamics within a single spring season at Lisbon Bottom in 1999. The study goal was to provide information necessary for resource managers to develop management strategies for this and other units of the Big Muddy National Fish and Wildlife Refuge. Researchers studied the hydrology, limnology, and biological dynamics of zooplankton, macroinvertebrates, fish and waterbird communities. Lisbon Bottom is one of several parcels of 1993 flood-damaged land that was purchased from willing sellers by the U.S. Fish and Wildlife Service as part of the Big Muddy National Fish and Wildlife Refuge. Lisbon Bottom is a loop bend in the river near Glasgow in Howard County, Missouri between approximately river mile (RM) 213 to RM 219. Flooding at Lisbon in 1993 and 1995 breeched local levees and created a diverse wetland complex.

Diseases of amphibians

Released July 01, 2020 15:37 EST

2007, ILAR Journal (48) 235-254

Christine L. Densmore, David E. Green

The development and refinement of amphibian medicine comprise an ongoing science that reflects the unique life history of these animals and our growing knowledge of amphibian diseases. Amphibians are notoriously fastidious in terms of captive care requirements, and the majority of diseases of amphibians maintained in captivity will relate directly or indirectly to husbandry and management. Investigators have described many infectious and noninfectious diseases that occur among various species of captive and wild amphibians, and there is considerable overlap in the diseases of captive versus free-ranging populations. In this article, some of the more commonly reported infectious and noninfectious diseases as well as their etiological agents and causative factors are reviewed. Some of the more common amphibian diseases with bacterial etiologies include bacterial dermatosepticemia or “red leg syndrome,” flavobacteriosis, mycobacteriosis, and chlamydiosis. The most common viral diseases of amphibians are caused by the ranaviruses, which have an impact on many species of anurans and caudates. Mycotic and mycotic-like organisms cause a number of diseases among amphibians, including chytridiomycosis, zygomycoses, chromomycoses, saprolegniasis, and ichthyophoniasis. Protozoan parasites of amphibians include a variety of amoeba, ciliates, flagellates, and sporozoans Common metazoan parasites include various myxozoans, helminths (particularly trematodes and nematodes), and arthropods. Commonly encountered non-infectious disease etiologies for amphibians include neoplasia, absolute or specific nutritional deficiencies or overloads, chemical toxicities, and inadequate husbandry or environmental management.

Physical habitat dynamics in four side-channel chutes, lower Missouri River

Released July 01, 2020 15:15 EST

2004, Open-File Report 2004-1071

Robert B. Jacobson, Harold E. Johnson, Mark S. Laustrup, Gary J. D'Urso, Joanna M. Reuter

Construction of the side-channel chutes has become a popular means to rehabilitate habitate of the Lower Missouri River. We studied various aspects of hydrology, hydraulics, and geomorphology of four side-channel chutes to document a range of existing conditions in the Lower Missouri River. The Cranberry Bend side-channel chute has existed for at least 40 years and is an example of a persistent, minimally engineered chute. The Lisbon Bottom side-channel chute is a young chute, created by extreme floods during 1993 – 1996, and allowed to evolve with minimum engineering of inlet and outlet structures. The Hamburg Bend and North Overton Bottom side-channel chutes were constructed in 1996 and 2000, respectively, as part of the Missouri River Bank Stabilization and navigation Fish and Wildlife Mitigation Project.

These side-channel chutes provide increased areas of sandbars and shallow, slow water – habitats thought to be substantially diminished in the modern Missouri River. Depths and velocities measured in side-channel chutes are also present in the main channel, but the chutes provide more areas of slow, shallow water and they increase the range of discharges over which shallow, slow water is present. The 3.6 km long Lisbon Bottom chute provides as much as 50% of the entire shallow water habitat that exists in the encompassing 15 km reach of the river. At Cranberry Bend and Lisbon Bottom, the side-channel chutes provided 10 – 40% of the availabile sandbar area in the reach, depending on discharge.

Each of the side-channel chutes shows evidence of continuing erosion and deposition. The longevity and the Cranberry Bend chute attests to dynamic stability – that is, a chute that maintains form and processes while shifting in position. The Hamburg chute similarly shows evidence of lateral movement and construction of flood plain to compensate for erosion. The Lisbon Bottom chute – the most intensively studied chute – appears to have achieved an equilibrium width and continues to migrate slowly; however, evidence of aggradation indicates that the chute has not reached an ultimate form, and may be continuing to adjust to altered hydrology and sediment availability. The North Overton Bottoms chute is the newest in the study. In its originally constructed form, the North Overton Bottoms pilot chute was extremely stable, even while being subjected to two floods in excess of 2-year recurrence interval and after accumulating large, potentially destabilizing large woody debris jams. Ongoing adaptive re-engineering of the North Overton Bottoms chute has prevented assessment of how the chute might have adjusted its form in the absence of intervention.

Assessment of Shallow-Water Habitat Availability in Modified Dike Structures, Lower Missouri River, 2004

Released July 01, 2020 15:00 EST

2004, Open-File Report 2004-1409

Robert B. Jacobson, Caroline M. Elliott, Harold E. Johnson III

This study documented the effects of wing-dike notching on the availabilit of shallow water habitat in the Lower Missouri River. Five wing dikes were surveyed in late May 2004 after they were notched in early May as part of shallow-water habitat (SWH) rehabilitation activities undertaken by the U.S. Army Corps of Engineers. Surveys included high-resolution hydroacoustic depth, velocity, and substrate mapping. Relations of bottom elevations within the wing dike fields to index discharges and water-surface elevations indicate that little habitat meeting the SWH definition was created immediately following notching. This result is not unexpected, as significant geomorphic adjustment may require large flow events. Depth, velocity, and substrate measurements in the post-rehabilitation time period provide baseline data for monitoring ongoing changes. Differences in elevation and substrate were noted at all sites. Most dike fields showed substantial aggradation and replacement of mud substrate with sandier sediment, although the changes did not result in increased availability of SWH at the index discharge. It is not known how much of the elevation and substrate changes can be attributed directly to notching and how much would result from normal sediment transport variation.

Aquatic habitat mapping with an acoustic doppler current profiler: Considerations for data quality

Released July 01, 2020 14:50 EST

2005, Open-File Report 2005-1163

David Gaeuman, Robert B. Jacobson

When mounted on a boat or other moving platform, acoustic Doppler current profilers (ADCPs) can be used to map a wide range of ecologically significant phenomena, including measures of fluid shear, turbulence, vorticity, and near-bed sediment transport. However, the instrument movement necessary for mapping applications can generate significant errors, many of which have not been inadequately described. This report focuses on the mechanisms by which moving-platform errors are generated, and quantifies their magnitudes under typical habitat-mapping conditions. The potential for velocity errors caused by mis-alignment of the instrument?s internal compass are widely recognized, but has not previously been quantified for moving instruments. Numerical analyses show that even relatively minor compass mis-alignments can produce significant velocity errors, depending on the ratio of absolute instrument velocity to the target velocity and on the relative directions of instrument and target motion. A maximum absolute instrument velocity of about 1 m/s is recommended for most mapping applications. Lower velocities are appropriate when making bed velocity measurements, an emerging application that makes use of ADCP bottom-tracking to measure the velocity of sediment particles at the bed. The mechanisms by which heterogeneities in the flow velocity field generate horizontal velocities errors are also quantified, and some basic limitations in the effectiveness of standard error-detection criteria for identifying these errors are described. Bed velocity measurements may be particularly vulnerable to errors caused by spatial variability in the sediment transport field.

Mapping vegetation communities in Ozark National Scenic Riverways: final technical report to the National Park Service

Released July 01, 2020 14:40 EST

2006, Open-File Report 2006-1354

Robert A. Chastain, Matthew A. Struckhoff, Keith W. Grabner, Esther D. Stroh, Hong He, David R. Larsen, Timothy A. Nigh, Jim Drake

Vegetation communities were mapped at two levels in Ozark National Scenic Riverways (ONSR) usign a hybrid combination of statistical methods and photointerpretation. The primary map includes 49 cover classes, including 24 cleasses that relate to vegetation associations currenly described by the United States National Vegetation Classification Standard (USNVC: The Nature Conservancy, 1994a). The remaining types include cultural features, ruderal communities on abandoned agricultural lands, and non-vegetated classes. Overall map classification accuarcy is 63 percent. The secondary mapping level aggregates communities with similar appearance and ecologically related associations into Community Types. The resultant 33-class Community Type map has an overall classification accuracy of 77 percent and identified groups of communities based on resource management goals within the park. Important additional products include 1) a general probability map for all vegetation associations, which can be used to assess final classification certainty, and 2) individual probability maps for each association, which can be used to identify areas that have a high likelihood of supporting a given type, beyond where that type was identified in the final map products. Other secondary map products include data layers derived from primary color-infrared imagery, secondary imagery data and digital elevation models. A field key and photo guide to associations and complete community descriptions were produced, along with a photo guide of fuel conditions. Wildland fuels data were used to generate a fuels map based upon Anderson's fuels models (1982).

Biomonitoring of Environmental Status and Trends (BEST) Program: Environmental contaminants and their effects on fish in the Rio Grande Basin

Released July 01, 2020 13:45 EST

2004, Scientific Investigations Report 2004-5108

Christopher J. Schmitt, Gail M. Dethloff, Jo Ellen Hinck, Timothy M. Bartish, Vicki Blazer, James J. Coyle, Nancy D. Denslow, Donald E. Tillitt

We collected, examined, and analyzed 368 fish of seven species from 10 sites in the Rio Grande Basin (RGB) during late 1997 and early 1998. Four sites were National Contaminant Biomonitoring Program (NCBP) stations where organochlorine ad elemental contaminants in fish had been monitored from 1969 and through 1986. The other six were USGS-National Stream Quantity Accounting Network (NASQAN) stations where water quality is monitored. The objectives were to document temporal and geographic trends in the concentrations of accumulative organic and inorganic contaminants in RGB fish and the effects of contaminants on the fish; to continue testing the feasibility of incorporating biomarkers (that is, biochemical, histopathological, and other biological indicators of contaminant exposure or effects) into a monitoring program for large U.S. rivers; and to evaluate the compatibility of monitoring methods based on the analysis of fish with those used to monitor water by NASQAN. Common carp (Cyprinus carpio; carp) and black basses (Micropterus sp.; bass) were the targeted species; together, they represented 77% of the fish collected. Each fish was examined in the field for externally and internally visible gross lesions, selected organs were weighed to compute various ponderal and organosomatic indices, and samples of tissues and fluids were obtained and preserved for analysis of fish health and reproductive biomarkers. Composite samples of whole fish from each station were grouped by species and gender and analyzed by instrumental methods for persistent organic and inorganic contaminants and for dioxin-like activity (TCDD-EQ) using the H4IIE rat hepatoma cell bioassay.

Biomonitoring of Environmental Status and Trends (BEST) Program: Environmental Contaminants and their Effects on Fish in the Columbia River Basin

Released July 01, 2020 13:20 EST

2004, Scientific Investigations Report 2004-5154

Jo Ellen Hinck, Christopher J. Schmitt, Timothy M. Bartish, Nancy D. Denslow, Vicki Blazer, Patrick J. Anderson, James J. Coyle, Gail M. Dethloff, Donald E. Tillitt

This project examined and analyzed 560 fish representing eight species from 16 sites in the Columbia River Basin (CRB) from September 1997 to April 1998. Ten of the 16 sampling locations were historical National Contaminant Biomonitoring Program (NCBP) sites where organochlorine and elemental contaminants in fish had been monitored from 1969 through 1986. Five sites were co-located at U.S. Geological Survey (USGS)-National Stream Quality Accounting Network (NASQAN) stations at which water quality is monitored. The sampling location at Marine Park in Vancouver, Washington did not correspond to either of the established monitoring programs. Eight of the sampling locations were located on the Columbia River; three were on the Snake River; two were on the Willamette River, and one site was on each of the Yakima, Salmon and Flathead Rivers.

Common carp (Cyprinus carpio), black basses (Micropterus sp.), and largescale sucker (Catostomus macrocheilus) together accounted for 80% of the fish sampled during the study. Fish were weighed and measured then field-examined for external and internal lesions, and liver, spleen, and gonads were weighed to compute somatic indices. Selected tissues and fluids were obtained and preserved for analysis of fish health and reproductive biomarkers. Composite samples of whole fish from each station were grouped by species and gender and analyzed for persistent organic and inorganic contaminants and for dioxin-like activity using H4IIE rat hepatoma cell bioassay.

A summary of water-quality monitoring in San Francisco Bay in water year 2017

Released July 01, 2020 12:33 EST

2020, Scientific Investigations Report 2020-5064

Daniel N. Livsey, Maureen A. Downing-Kunz

This report summarizes the activities of the U.S. Geological Survey (USGS) San Francisco Bay Water-Quality Monitoring and Sediment Transport Project during water year 2017, including an explanation of methods employed, stations operated, and a graphical summary of data for the period of record for stations operational in water year 2017. In cooperation with partner agencies, the USGS maintains a network of sensors that continuously and autonomously measures water-quality parameters in San Francisco Bay including water temperature, specific conductance, turbidity, and suspended-sediment concentration. Data are collected at several locations in the estuary by a network of water-quality sondes sampled at 15-minute intervals. Methods of data collection are presented along with documentation of the regression models utilized to estimate suspended-sediment concentration from observed turbidity, a commonly utilized surrogate to estimate suspended-sediment concentration. The goals of the data collection effort are to (1) obtain long-term, high-frequency, and high-quality data to describe San Francisco Bay water quality; (2) make the data publicly available on the USGS National Water Information System data portal; and (3) help improve understanding of the spatial and temporal variability of water quality in the estuary, informing management decisions regarding restoration, water supply, navigation, and ecology.

Development of an approach for integrating components of the U.S. Geological Survey Biomonitoring of Environmental Status and Trends (BEST) and National Stream Quantity Accounting Network (NASQAN) programs for large U.S. rivers

Released July 01, 2020 12:30 EST

2005, Scientific Investigations Report 2005-5083

Nancy J. Bauch, Christopher J. Schmitt, Charles G. Crawford

A national-scale framework for monitoring environmental contaminants in fish and effects of contaminant exposure on fish in large U.S. rivers has been proposed by the Biomonitoring of Environmental Status and Trends (BEST) Program of the U.S. Geological Survey (USGS). The framework shares many features and objectives with the USGS National Stream Quantity Accounting Network (NASQAN) Program, which monitors water quality in large U.S. river basins–those with drainage areas of 250,000 to 1,200,000 square miles at their most downstream stations. Because the two programs appear to be complementary, this study was initiated in 2001 to investigate alternative techniques for summarizing and integrating the water-quality data with the fish-contaminant and fish-health data, and to provide recommendations to the BEST program for future integrated studies.

Elevation-derived hydrography acquisition specifications

Released July 01, 2020 11:58 EST

2020, Techniques and Methods 11-B11

Silvia Terziotti, Christy-Ann Archuleta

Hydrographic features derived from U.S. Geological Survey (USGS) 3D Elevation Program data, and collected for use by the USGS, must meet the specifications described in this document. The specifications described herein pertain to the final product delivered to the USGS, not to methods used to derive the hydrographic features. The specifications describe the collection area, spatial reference system, attribute table structure, feature codes and values, delineation of hydrographic features, topology, positional assessment, metadata, and delivery formats. A companion document, Elevation-Derived Hydrography—Representation, Extraction, Attribution, and Delineation Rules, defines the fields, domains, and minimum feature collection requirements for hydrography features derived from elevation data. Hydrographic features collected to this specification will be suitable for using as breaklines to hydroflatten digital elevation models, processing for preconflation of features to the National Hydrography Dataset, and using for hydroenforcement of digital elevation models.

Elevation-derived hydrography—Representation, extraction, attribution, and delineation rules

Released July 01, 2020 11:56 EST

2020, Techniques and Methods 11-B12

Christy-Ann Archuleta, Silvia Terziotti

With the increasing availability of 3D Elevation Program (3DEP) quality high resolution elevation data across the United States and the pressing need for better integrated elevation and hydrography data, the U.S. Geological Survey is developing guidance to improve the horizontal and vertical alignment of these datasets. The U.S. Geological Survey is providing the Elevation-Derived Hydrography—Acquisition Specifications for the acquisition of elevation-derived hydrography for the United States, and the companion document The Elevation-Derived Hydrography—Representation, Extraction, Attribution, and Delineation (READ) Rules, which describes the parameters for the portrayal of hydrography features as derived from elevation data. The READ Rules provide a definition, example, attribute value list, delineation instructions, representation rules, and data extraction rules for each hydrography feature required to meet the Elevation-Derived Hydrography—Acquisition Specifications.

Community for data integration 2018 funded project report

Released June 30, 2020 14:15 EST

2020, Open-File Report 2020-1062

Leslie Hsu, Caitlin M. Andrews, John B. Bradford, Daniel D. Buscombe, Katherine J. Chase, Wesley M. Daniel, Jeanne M. Jones, Pam Fuller, Benjamin B. Mirus, Matthew E. Neilson, Hans W. Vraga, Jessica J. Walker, Dennis H. Walworth, Jonathan Warrick, Jake Weltzin, Daniel J. Wieferich, Nathan J. Wood

The U.S. Geological Survey Community for Data Integration annually funds small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 10 projects funded in fiscal year 2018, outlining their goals, activities, and accomplishments.

Frequency of extreme freeze events controls the distribution and structure of black mangroves (Avicennia germinans) near their northern range limit in coastal Louisiana

Released June 29, 2020 13:31 EST

2020, Diversity and Distributions

Michael Osland, Richard Day, Thomas C. Michot


Climate change is expected to result in the tropicalization of coastal wetlands in the northern Gulf of Mexico, as warming winters allow tropical mangrove forests to expand their distribution poleward at the expense of temperate salt marshes. Data limitations near mangrove range limits have hindered understanding of the effects of winter temperature extremes on mangrove distribution and structure. Here, we investigated the influence of extreme freeze events on the abundance, height and coverage of black mangroves (Avicennia germinans ) near their northern range limit in Louisiana.


Coastal Louisiana, USA.


We quantified the relationships between the frequency of extreme freeze events and A. germinans abundance, height and coverage using: (a) mangrove observation points recorded via aerial surveys from a fixed‐wing aircraft; (b) 30 years of temperature data; and (c) mangrove mortality and leaf damage temperature thresholds. We used freeze frequency data and mangrove–climate relationships to evaluate and spatially depict the risk of A. germinans freeze damage across Louisiana.


We identified strong negative relationships between the frequency of extreme freeze events and A. germinans abundance, height and coverage. Avicennia germinans is most abundant, tall and continuous along the south‐eastern outer coast of Louisiana, where the frequency of extreme freeze events is reduced (i.e., lower risk of mangrove freeze damage) by the buffering effects of comparatively warm Gulf of Mexico waters. Conversely, the risk of A. germinans freeze damage has historically been very high across Louisiana's Chenier Plain and within more inland wetlands in the Deltaic Plain.

Main conclusions

Our analyses advance understanding of how the frequency of extreme freeze events controls the distribution, height and coverage of A. germinans near its northern range limit. In addition to informing climate‐smart coastal restoration efforts, our findings can be used to better anticipate and prepare for the tropicalization of temperate wetlands due to climate change.

After-hatch and hatch year Buff-breasted Sandpipers (Calidris subruficollis) can be sexed accurately using morphometric measures

Released June 29, 2020 09:37 EST

2020, Wader Study (127) 37-42

Juliana B. Almeida, Iara F. Lopes, Lewis Oring, Lee Tibbitts, Lisa M. Pajot, Richard B. Lanctot

Determining the sex of birds quickly in the field can help in studies of behavior and distribution, and when selecting particular sexes for deploying tracking devices or collecting samples. However, discerning males from females is difficult in species that are plumage monomorphic and have overlapping sexual-size dimorphism, as in Buff-breasted Sandpipers Calidris subruficollis. We developed three discriminant functions to sex Buff-breasted Sandpipers based on measurements of live birds captured in Brazil whose sex was confirmed with molecular techniques. We validated these discriminant functions using morphometric measures from other independent samples of known-sex live birds from wintering (Brazil), migration (Texas), and breeding (Alaska) sites. Discriminant functions derived from birds captured in Brazil accurately sexed ≥88% of the validation sample from Brazil, Texas, and Alaska. Errors in classification occurred among males on the wintering (0–5%) and breeding (8–12%) grounds, and females during migration (0–11%). Discriminant functions worked well because of the substantial sexual size dimorphism present in the species, with male traits being in general 5.2–10.4% larger than female traits. The size of morphological traits did not vary by age (after controlling for sex) for birds sampled on the wintering grounds and during migration. Our results indicate that discriminant functions can be used to sex after-hatch year (AHY) Buff-breasted Sandpipers throughout their range, and for hatch year (HY) birds during their first southbound migration and winter. Being able to accurately sex both AHY and HY birds using only morphological measurements will improve studies of the ecology and population structure of this species and enhance the application of conservation measures.

Refining genetic boundaries for Agassiz’s desert tortoise (Gopherus agassizii) in the western Sonoran Desert: The influence of the Coachella Valley on gene flow among populations in southern California

Released June 29, 2020 09:08 EST

2020, Frontiers of Biogeography

Jeffrey E. Lovich, Taylor Edwards, Kristin H. Berry, Shellie R. Puffer, Kristy L. Cummings, Ennen Joshua R., Mickey Agha, Rachel Woodard, Kathleen D. Brundige, Robert W. Murphy

(Lovich) Understanding the influence of geographic features on the evolutionary history and population structure of a species can assist wildlife managers in delimiting genetic units (GUs) for conservation and management. Landscape features including mountains, low elevation depressions, and even roads can influence connectivity and gene flow among Agassiz’s desert tortoise (Gopherus agassizii) populations. Substantial changes in the landscape of the American Southwest occurred during the last six million years (including the formation of the Gulf of California and the lower Colorado River), which shaped the distribution and genetic structuring of tortoise populations. The area northwest of the Gulf of California is occupied by the Salton Trough, including the Coachella Valley at its northern end. Much of this area is below sea level and unsuitable as tortoise habitat, thus forming a potential barrier for gene flow. We assessed genetic relationships among three tortoise populations separated by the Coachella Valley. Two adjacent populations were on the east side of the valley in the foothills of the Cottonwood and Orocopia mountains separated by Interstate 10. The third population, Mesa, was located about 87 km away in the foothills of the San Bernardino Mountains at the far northwestern tip of the valley. The Cottonwood and Orocopia localities showed genetic affiliation with the adjacent Colorado Desert GU immediately to the east, and the Mesa population exhibited affiliation with both the Southern Mojave and Colorado Desert GUs, despite having a greater geographic distance (0.5x–1.5x greater) to the Colorado Desert GU. The genetic affiliation with the Colorado Desert GU suggests that the boundary for that GU needs to be substantially extended to the west to include the desert tortoise populations around the Coachella Valley. Their inclusion in the Colorado Desert GU may benefit these often overlooked populations when recovery actions are considered.

Changes in capture rates and body size among vertebrate species occupying an insular urban habitat reserve

Released June 29, 2020 07:48 EST

2020, Conservation Science and Practice

Thomas Stanley, Rulon W. Clark, Robert N. Fisher, Carlton J. Rochester, Stephanie A Root, Keith J Lombardo, Stacey D Ostermann-Kelm

Long‐term ecological monitoring provides valuable and objective scientific information to inform management and decision‐making. In this article, we analyze 22 years of herpetofauna monitoring data from the Point Loma Ecological Conservation Area (PLECA), an insular urban reserve near San Diego, CA. Our analysis showed that counts of individuals for one of the four most common terrestrial vertebrates declined, whereas counts for other common species increased or remained stable. Two species exhibited declines in adult body length, whereas biomass pooled over the five most common species increased over time and was associated with higher wet season precipitation. Although the habitat and vegetation at PLECA have remained protected and intact, we suspect that changes in arthropod communities may be driving changes in the abundance, growth, and development of insectivorous lizards. This study underscores the value of long‐term monitoring for establishing quantitative baselines to assess biological changes that would otherwise go undetected.

A rasterized building footprint dataset for the United States

Released June 29, 2020 07:16 EST

2020, Scientific Data (7)

Mehdi Pourpeikari Heris, Nathan Leon Foks, Kenneth J. Bagstad, Austin Troy, Zachary H. Ancona

Microsoft released a U.S.-wide vector building dataset in 2018. Although the vector building layers provide relatively accurate geometries, their use in large-extent geospatial analysis comes at a high computational cost. We used High-Performance Computing (HPC) to develop an algorithm that calculates six summary values for each cell in a raster representation of each U.S. state, excluding Alaska and Hawaii: (1) total footprint coverage, (2) number of unique buildings intersecting each cell, (3) number of building centroids falling inside each cell, and area of the (4) average, (5) smallest, and (6) largest area of buildings that intersect each cell. These values are represented as raster layers with 30 m cell size covering the 48 conterminous states. We also identify errors in the original building dataset. We evaluate precision and recall in the data for three large U.S. urban areas. Precision is high and comparable to results reported by Microsoft while recall is high for buildings with footprints larger than 200 m2 but lower for progressively smaller buildings.

Using saline or brackish aquifers as reservoirs for thermal energy storage, with example calculations for direct-use heating in the Portland Basin, Oregon, USA

Released June 28, 2020 07:32 EST

2020, Geothermics (88)

Erick Burns, John Bershaw, Colin F. Williams, Ray E Wells, Matt W Uddenberg, Darby P Scanlon, Trenton T Cladouhos, Boz Van Houten

Boz Van Houten, editor(s)

Tools to evaluate reservoir thermal energy storage (RTES; heat storage in slow-moving or stagnant geochemically evolved permeable zones in strata that underlie well-connected regional aquifers) are developed and applied to the Columbia River Basalt Group (CRBG) beneath the Portland Basin, Oregon, USA. The performance of RTES for heat storage and recovery in the Portland Basin is strongly dependent on the operational schedule of heat injection and extraction. We examined the effects of the operational schedule, based on an annual solar hot water supply pattern and a building heating demand model, using heat and fluid flow simulations with SUTRA. We show RTES to be feasible for supply of heating energy for a large combined research/teaching building on the Oregon Health and Science University South Waterfront expansion, an area of planned future development. Initially, heat is consumed to increase the reservoir temperature, and conductive heat loss is high due to high temperature gradients between the reservoir and surrounding rock. Conductive heat loss continues into the future, but the rate of heat loss decreases, and heat recovery efficiency of the RTES system increases over time. Simulations demonstrate the effects of varying heat-delivery rate and temperature on the heat production history of the reservoir. If 100% of building heating needs are to be supplied by combined solar/RTES, then the solar system must be sized to meet building needs plus long-term thermal losses (i.e., conductive losses once the system is heated to pseudo-steady state) from the RTES system. If the solar heating system barely meets these criteria, then during early years, less than 100% of the building demand will be supplied until the reservoir is fully-heated. The duration of supplying less than 100% of building demand can be greatly shortened by pre-heating the reservoir before building heating operations or by adding extra heat from external sources during early years. Analytic solutions are developed to evaluate efficacy and to help design RTES systems (e.g., well-spacing, thermal source sizing, etc.). A map of thermal energy storage capacity is produced for the CRBG beneath the Portland Basin. The simulated building has an annual heat load of ∼1.9 GWh, and the total annual storage capacity of the Portland Basin is estimated to be 43,400 GWh assuming seasonal storage of heat yields water from which 10 °C can be extracted via heat exchange, indicating a tremendous heating capacity of the CRBG.

    Near-term spatial hydrologic forecasting in Everglades, USA for landscape planning and ecological forecasting

    Released June 27, 2020 10:27 EST

    2020, Environmental Modelling and Software

    Leonard G. Pearlstine, James M. Beerens, Gregg Reynolds, Saira Haider, James M. McKelvy, Kevin Suir, Stephanie Romanach, Jennifer H. Nestler

    Operational ecological forecasting is an emerging field that leverages ecological models in a new, cross-disciplinary way – using a real-time or nearly real-time climate forecast to project near-term ecosystem states. These applications give decision-makers lead time to anticipate and manage state changes that degrade ecosystem functions or directly impact humans. The Everglades Forecasting model (EverForecast) is an operational forecast model designed specifically for conservation management purposes including water management. It provides up to six-month forecasts of daily projected, spatially continuous stage values across the Everglades. We validated EverForecast quarterly to measured historical values at 207 gages (1 Jan 2000 – 31 Dec 2019). EverForecast hindcasted water stage accurately captured measured stage variation, with a low percentage of measured stage exceeding hindcasted values. Over the whole spatial extent, the mean RMSE is 20.98 cm, the mean MAE is 14.42 cm, and the mean MBE is 0.91 cm.

    Procedure for calculating estimated ultimate recoveries of wells in the Wolfcamp shale of the Midland Basin, Permian Basin Province, Texas

    Released June 26, 2020 13:50 EST

    2020, Scientific Investigations Report 2020-5042

    Heidi M. Leathers-Miller

    In 2016, the U.S. Geological Survey published an assessment of technically recoverable continuous oil and gas resources of the Wolfcamp shale in the Midland Basin, Permian Basin Province, Texas. Estimated ultimate recoveries (EURs) were calculated with production data from IHS MarkitTM using DeclinePlus software in the Harmony interface. These EURs were a major component of the quantitative resource assessment. For five of the six assessment units in the study, an industry operator in the Midland Basin provided information that was used to differentiate the Wolfcamp horizontal well landing zones. The IHS MarkitTM production database does not distinguish between the Wolfcamp A, B, C, and D well landing zones. These different units of the Wolfcamp have different production patterns that are important for calculation of EURs. The calculated mean EURs for each assessment unit ranged from 99,000 barrels of oil in the Wolfcamp C to 142,000 barrels of oil in the Wolfcamp A.

    Supporting natural resource-management decisions—The role of economics at the U.S. Department of the Interior (DOI)—2018 DOI Economics Training Workshop

    Released June 26, 2020 10:15 EST

    2020, Open-File Report 2020-1044

    Mustapha Alhassan, Emily J. Pindilli, Christian S.L. Crowley, Carl D. Shapiro, Benjamin M. Simon

    The second U.S. Department of the Interior (DOI) Economics Training Workshop (hereafter “Workshop”) was held during September 25–27, 2018, in Washington, D.C., to identify, highlight, and better understand needs and opportunities for economic analysis to support DOI’s mission. Building on the first workshop in 2017, the second Workshop, jointly convened by the DOI Office of Policy Analysis and the U.S. Geological Survey (USGS) Science and Decisions Center, provided an opportunity for DOI economists to share expertise and experiences and to build collaboration and communication channels across DOI. In addition, the second Workshop provided training sessions on a variety of relevant economic and modeling topics. More than 40 DOI economists gathered at the Workshop to share their work, discuss shared challenges, and identify approaches to advance the use and contribution of economics at the DOI.

    Mitochondrial genome diversity and population mitogenomics of Polar cod (Boreogadus saida) and Arctic dwelling gadoids

    Released June 26, 2020 09:39 EST

    2020, Polar Biology

    Robert E. Wilson, Sarah A. Sonsthagen, Noel Sme, Anthony J. Gharrett, Andrew Majewski, Kate Wedemeyer, R. John Nelson, Sandra L. Talbot

    High-latitude fish typically exhibit a narrow thermal tolerance window, which may pose challenges when coping with temperatures that shift outside of a species’ range of tolerance. Due to its role in aerobic metabolism and energy balance, the mitochondrial genome is likely critical for the acclimation and adaptation to differing temperature regimes in marine ectotherms. As oceans continue to warm, there is growing need to understand the ability of organisms to respond to changing environmental conditions given evidence that some species, in particular cold-water species, may already be experiencing difficulties. To assess how Arctic gadids in Alaska have responded to differential thermal preferences in the past and how regions are interconnected, we sequenced complete mitochondrial genomes for four Arctic gadids to determine the distribution of mitochondrial diversity and population-level structure as well as to detect signatures of selection acting on mitochondrial genome. We found little population level structure within all four species with the clear exception of Gulf of Alaska Saffron cod (Eleginus gracilis). Northern localities exhibited higher levels of genetic diversity and primarily northern lineages were observed within Polar (Boreogadus saida) and Saffron cod, likely reflecting asymmetrical dispersal and potentially admixture of distinct lineages via ocean currents. The main evolutionary force shaping the evolution of the mitogenome appears to be purifying selection, but we also identified potential positive selection of candidate amino acid replacements primarily in Complex I (ND genes) in Polar cod. The high levels of mitochondrial diversity observed in our study and large population size may provide this species with the ability to respond evolutionarily (i.e. long-term) to a changing environment.

    Migratory behavior and winter geography drive differential range shifts of eastern birds in response to recent climate change

    Released June 26, 2020 08:36 EST

    2020, Proceedings of the National Academy of Sciences of the United States of America (117) 12897-12903

    Clark Rushing, Andy Royle, David Ziolkowski Jr., Keith L. Pardieck

    Over the past half century, migratory birds in North America have shown divergent population trends relative to resident species, with the former declining rapidly and the latter increasing. The role that climate change has played in these observed trends is not well understood, despite significant warming over this period. We used 43 y of monitoring data to fit dynamic species distribution models and quantify the rate of latitudinal range shifts in 32 species of birds native to eastern North America. Since the early 1970s, species that remain in North America throughout the year, including both resident and migratory species, appear to have responded to climate change through both colonization of suitable area at the northern leading edge of their breeding distributions and adaption in place at the southern trailing edges. Neotropical migrants, in contrast, have shown the opposite pattern: contraction at their southern trailing edges and no measurable shifts in their northern leading edges. As a result, the latitudinal distributions of temperate-wintering species have increased while the latitudinal distributions of neotropical migrants have decreased. These results raise important questions about the mechanisms that determine range boundaries of neotropical migrants and suggest that these species may be particularly vulnerable to future climate change. Our results highlight the potential importance of climate change during the nonbreeding season in constraining the response of migratory species to temperature changes at both the trailing and leading edges of their breeding distributions. Future research on the interactions between breeding and nonbreeding climate change is urgently needed.

    Changes to Monitoring Trends in Burn Severity Program’s production procedures and data products

    Released June 26, 2020 08:29 EST

    2020, Fire Ecology (16)

    Joshua J. Picotte, Krishna P. Bhattarai, Daniel Howard, Jennifer Lecker, Justin Epting, Brad Quayle, Nate Benson, Kurtis Nelson

    The Monitoring Trends in Burn Severity (MTBS) program has been providing the fire science community with large fire perimeter and burn severity data for the past 14 years. As of October 2019, 22 969 fires have been mapped by the MTBS program and are available on the MTBS website ( These data have been widely used by researchers to examine a variety of fire and climate science topics. However, MTBS has undergone significant changes to its fire mapping methodology, the remotely sensed imagery used to map fires, and the subsequent fire occurrence, burned boundary, and severity databases. To gather a better understanding of these changes and the potential impacts that they may have on the user community, we examined the changes to the MTBS burn mapping protocols and whether remapped burned area boundary and severity products differ significantly from the original MTBS products.

    Reduction in drinking water arsenic exposure and health risk through arsenic treatment among private well households in Maine and New Jersey, USA

    Released June 26, 2020 08:24 EST

    2020, Science of the Total Environment (738)

    Qiang Yang, Sara V. Flanagan, Steven Chillrud, James Ross, Wenke Zeng, Charles W. Culbertson, Steve Spayd, Lorraine C. Backer, Andrew E. Smith, Yan Zheng

    Over 2 million people in the United States (U.S.) drink water from private wells that contain arsenic (As) exceeding the U.S. Environmental Protection Agency (USEPA) Maximum Contaminant Level (MCL) of 10 micrograms per liter (μg/L). While there are a number of commercially available treatment technologies for removing As from drinking water, it is up to the private well households to decide whether to treat for As or not. However, how well existing treatment technologies perform in real world situations, and to what extent they reduce health risks, are not well understood. This study evaluates the effectiveness of household As treatment systems in southern-central Maine (ME, n=156) and northern New Jersey (NJ, n=94) and ascertains how untreated well water chemistry and other factors influence As removal. Untreated and treated water samples, as well as a treatment questionnaire, were collected. Most ME households in this study had point-of-use reverse-osmosis systems (POU RO), while in NJ, dual-tank point-of-entry (POE) whole house systems were popular. Arsenic treatment systems reduced well water arsenic concentrations ([As]) by up to two orders of magnitude, i.e. from a median of 71.7 to 0.8 μg/L and from a mean of 105 to 14.3 μg/L in ME, and from a median of 8.6 to 0.2 μg/L and a mean of 15.8 to 2.1 μg/L in NJ. More than half (53%) of the systems in ME reduced water [As] to below 1 µg/L, compared to 69% in NJ. The treatment system failure rates were 19% in ME (> USEPA MCL 10 µg/L) and 16% in NJ (> NJ standard 5 μg/L). In both states, the higher the untreated well water [As] and the As(III)/As ratio, the higher the rate of treatment failure. POE systems failed less than POU systems, as did the treatment systems installed and maintained by vendors than those by homeowners. The 7-fold reduction of [As] in the treated water reduced skin cancer risk alone from 3,765 to 514 in 1 million in ME, and from 568 to 75 in 1 million in NJ.

    Small gradients in salinity have large effects on stand water use in freshwater wetland forests

    Released June 25, 2020 07:42 EST

    2020, Forest Ecology and Management (473)

    Jamie A. Duberstein, Ken Krauss, M.J. Baldwin, Scott T. Allen, William H. Conner, John S. Salter, Michael Miloshis

    Salinity intrusion is responsible for changes to freshwater wetland watersheds globally, but little is known about how wetland water budgets might be influenced by small increments in salinity. We studied a forested wetland in South Carolina, USA, and installed sap flow probes on 72 trees/shrubs along a salinity gradient. Species investigated included the trees baldcypress (Taxodium distichum [L.] Rich.), water tupelo (Nyssa aquatica L.), swamp tupelo (Nyssa biflora Walt.), and the shrub waxmyrtle (Morella cerifera (L.) Small). This study improves upon past reliance on greenhouse seedling studies by adding measurements of trees/shrubs along a salinity gradient, and better describes the role of low salinity on water use in freshwater wetland forests. We measured patterns of water use related to salinity, atmospheric conditions and season, and hypothesized that salinity would influence wetland forest water use through two mechanisms: salinity disturbances would yield stands with species and size classes that transpire less and individual trees with less conductive xylem tissue (i.e., sapwood). Both hypotheses held. At salinity concentrations ranging from fresh to 3 psu, forest structural changes alone resulted in stand water use reductions from 494 mm year-1 in freshwater stands to 316 mm year-1 in stands of slightly higher salinity. Tree sapwood function (inferred from radial sap flux profiles) also changed along this gradient and reduced sap flow rates by an additional 13.3% per unit increase in salinity (psu). Thus, stand water use was further reduced to 190 mm year-1 on saline sites. We found that forest structure is not the only change that affects water use in salinized watersheds; individual tree eco-physiological responses to salinity, manifesting in different radial sap flow profiles, are important as well.

      Highly competent native snake hosts extend the range of an introduced parasite beyond its invasive Burmese python host

      Released June 24, 2020 12:18 EST

      2020, Ecosphere (11)

      Melissa A. Miller, John M. Kinsella, Ray W. Snow, Bryan G. Falk, Robert Reed, Scott M. Goetz, Frank J. Mazzotti, Craig Guyer, Christina M. Romagosa

      Invasive Burmese pythons (Python bivittatus ) have introduced a nonnative pentastomid parasite (Raillietiella orientalis ) to southern Florida that has spilled over to infect native snakes. However, the extent of spillover, regarding prevalence and intensity, is unknown. We examined native snakes (n  = 523) and invasive pythons (n  = 1003) collected from Florida to determine the degree to which parasite spillover is occurring. We found R. orientalis has infected 13 species of native snakes collected from areas of sympatry with pythons. Prevalence and infection intensity of R. orientalis were significantly higher among native snakes compared with pythons. Moreover, adult female pentastomes achieved larger sizes and represented a greater proportion of the overall parasite population in native snakes vs. pythons, indicating native snakes are more competent hosts of R. orientalis than pythons. We also examined native snakes from regions of allopatry with pythons to determine how far R. orientalis has spread. We found an infected native snake 348 km north of the northernmost infected python. Our data show that native snakes are highly competent hosts of R. orientalis and have facilitated the rapid spread of this nonnative pentastome beyond the range of its invasive host.

      Graphical Dispersion Plot Editor (DPE) for seismic-site characterization by using multiple surface-wave methods

      Released June 24, 2020 11:36 EST

      2020, Open-File Report 2020-1065

      Devin McPhillips, Alan K. Yong, Antony Martin, William J. Stephenson


      To understand the behavior of potentially damaging ground motions during earthquakes, seismic-site effects are routinely characterized by using the dispersion of surface waves. Many methods exist to measure dispersion; these methods have various advantages and disadvantages, but they all yield dispersion data that must be inverted for shear-wave velocity. This report presents a graphical tool for efficiently removing spurious data as well as combining data from multiple methods prior to inversion.

      The Dispersion Plot Editor (DPE) program presented here (version 1.5) is coded in Python 3, which is open source and platform independent. DPE accepts input dispersion data as one or more delimited text files. The program plots the data in useful forms, including both scattered points and an interpolated heat map. The user selects points to delete by drawing arbitrary shapes with the mouse cursor. After the spurious data are removed, the user may represent the acceptable data with a dispersion curve. The acceptable data and the representative dispersion curve are output as separate comma-delimited text files. Images of the plotted data and the representative dispersion curve may also be saved.

      The effects of management practices on grassland birds—LeConte’s Sparrow (Ammospiza leconteii)

      Released June 23, 2020 10:42 EST

      2020, Professional Paper 1842-JJ

      Jill A. Shaffer, Lawrence D. Igl, Douglas H. Johnson, Marriah L. Sondreal, Christopher M. Goldade, Amy L. Zimmerman, Betty R. Euliss

      Keys to LeConte’s Sparrow (Ammospiza leconteii) management include controlling succession and providing uplands and lowlands with tall, thick herbaceous vegetation and thick litter. LeConte’s Sparrows have been reported to use habitats with 30–90 centimeters (cm) average vegetation height, 19–41 cm visual obstruction reading, 35–43 percent grass cover, 16–27 percent forb cover, less than (<) 18 percent shrub cover, <4 percent bare ground, 39–45 percent litter cover, and 2–6 cm litter depth.

      The predictive skills of elastic Coulomb rate-and-state aftershock forecasts during the 2019 Ridgecrest, California, earthquake sequence

      Released June 23, 2020 10:23 EST

      2020, Bulletin of the Seismological Society of America

      Simone Mancini, Margarita Segou, Maximillian J Werner, Thomas E. Parsons

      Operational earthquake forecasting protocols commonly use statistical models for their recognized ease of implementation and robustness in describing the short-term spatiotemporal patterns of triggered seismicity. However, recent advances on physics-based aftershock forecasting reveal comparable performance to the standard statistical counterparts with significantly improved predictive skills when fault and stress field heterogeneities are considered. Here, we perform a pseudo-prospective forecasting experiment during the first month of the 2019 Ridgecrest (California) earthquake sequence. We develop seven Coulomb rate-and-state models that couple static stress change estimates with continuum mechanics expressed by the rate-and-state friction laws. Our model parametrization supports a gradually increasing complexity; we start from a preliminary model implementation with simplified slip distributions and spatially homogeneous receiver faults to reach an enhanced one featuring optimized fault constitutive parameters, finite-fault slip models, secondary triggering effects, and spatially heterogenous planes informed by pre-existing ruptures. The data-rich environment of Southern California allows us to test whether incorporating data collected in near real-time during an unfolding earthquake sequence boosts our predictive power. We assess the absolute and relative performance of the forecasts by means of statistical tests used within the Collaboratory for the Study of Earthquake Predictability (CSEP) and compare their skills against a standard benchmark ETAS model for the short (24 hours after the two Ridgecrest mainshocks) and intermediate-term (one month). Stress-based forecasts expect heightened rates along the whole near-fault region and increased expected seismicity rates in Central Garlock Fault. Our comparative model evaluation supports that faulting heterogeneities coupled with secondary triggering effects are the most critical success components behind physics-based forecasts, but also underlines the importance of model updates incorporating near real-time available aftershock data reaching better performance than ETAS models. We explore the physical basis behind our results by investigating the localized shut down of pre-existing normal faults in the Ridgecrest near-source area.

      NHDPlus High Resolution (NHDPlus HR)---A hydrography framework for the Nation

      Released June 23, 2020 09:20 EST

      2020, Fact Sheet 2020-3033

      Susan G. Buto, Rebecca D. Anderson

      Reliable and accurate high-resolution mapping of the Nation’s waters are critical inputs to models and decision support systems used to predict risk and enable response to impacts on water resources. It is necessary to know where the water is and how it relates to features beyond the stream network like forests, cities, and infrastructure. An up-to-date, high-resolution national hydrography framework is required for modeling the occurrence of water and to provide the ability to connect detailed information from the surrounding landscape to the stream network. To support this, the U.S. Geological Survey is developing NHDPlus High Resolution (NHDPlus HR), the next generation of NHDPlus using updated, high-resolution datasets to create a modern, scalable, and openly accessible hydrography framework for the inland waters of the Nation.

      Hydrodynamic modeling results showing the effects of the Luce Bayou interbasin transfer on salinity in Lake Houston, TX

      Released June 23, 2020 08:45 EST

      2020, Texas Water Journal (11) 64-88

      Erik A. Smith, Sachin D. Shah

      An overreliance on groundwater resources in the Houston (Texas) metropolitan area led to aquifer drawdowns and land subsidence, so regional water suppliers have been turning to surface water resources to meet water demand. Lake Houston, an important water supply reservoir 24 kilometers (15 miles) northeast of downtown Houston, requires new water supply sources to continue to meet water supply demands for the next several decades. The upcoming Luce Bayou Interbasin Transfer Project will divert up to 500 million gallons per day of Trinity River water into Lake Houston. Trinity River water has significantly different water quality than the Lake Houston tributaries. To evaluate the project’s potential effect on water quality, the U.S. Geological Survey used an enhanced version of a previously released Lake Houston hydrodynamic model. With a focus on salinity and water-surface elevations, the model combined data from 2009 to 2017 with simulated flow from the Luce Bayou Interbasin Transfer to evaluate potential outcomes from three hypothetical flow scenarios. Overall, these scenarios found that the Luce Bayou Interbasin Transfer would cause salinities to moderately over most of the modeled time (2009–2017), although salinities were buffered under 2011 drought conditions. Large inflow events equalized salinities under baseline conditions as well as the enhanced flow scenarios.

      Surface displacement distributions for the July 2019 Ridgecrest, California earthquake ruptures

      Released June 23, 2020 07:55 EST

      2020, Bulletin of the Seismological Society of America

      Christopher Duross, Ryan D. Gold, Timothy E. Dawson, Katherine Scharer, Katherine Kendrick, Sinan Akciz, Stephen J. Angster, Jeffery Bachhuber, Steven Bacon, Scott E. K. Bennett, Luke Blair, Benjamin A. Brooks, Thomas Bullard, W. Paul Burgess, Colin Chupik, Michael DeFrisco, Jaime Delano, James D. Dolan, Erik Frost, Nick Graehl, Elizabeth Haddon, Alexandra Elise Hatem, Janis Hernandez, Christopher S. Hitchcock, Kennth Hudnut, Jessica Thompson Jobe, Richard D Koehler, Ozgur Kozaci, Tyler C. Ladinsky, Christopher Madugo, Devin McPhillips, Christopher Milliner, Alexander Morelan, Brian Olson, Jason Patton, Belle Philibosian, Alexandra J. Pickering, Ian Pierce, Daniel J. Ponti, Gordon G. Seitz, Eleanor Spangler, Brian J. Swanson, Kate Thomas, Jerome Treiman, Francesca Valencia, Alana Williams, Robert Zinke

      The 2019 Ridgecrest, California earthquake sequence generated surface fault rupture along two orthogonal cross faults, including the dominantly left-lateral and northeast-striking Mw6.4 rupture and dominantly right-lateral and northwest-striking Mw7.1 rupture. We present >650 field-based surface-displacement observations for these ruptures, calculate displacement curves, and synthesize our results into cumulative along-strike displacement distributions. Using these data, we calculate displacement gradients and compare our results with historical ruptures in the Eastern California Shear Zone. For the M6.4 rupture, we report 96 displacements measured along 18 km of northeast-striking rupture. Cumulative displacement curves for the rupture yield a mean left-lateral displacement of 0.30.5 m and maximum of 0.71.6 m. Net mean vertical displacement based on the difference of down-to-the-west and down-to-the-east displacement curves is close to zero (0.02 m down-to-the-west). The M6.4 displacement distribution shows that the majority of displacement occurred southwest of the intersection with the M7.1 rupture. The M7.1 rupture is northwest-striking and 50 km long based on 576 field measurements. Displacement curves indicate a mean right-lateral displacement of 1.21.7 m and a maximum of 4.37.0 m. Net vertical displacement in the rupture averages 0.3 m down-to-the-west. The M7.1 displacement distributions demonstrate that maximum displacement occurred ~23 km SE of the M7.1 epicenter, releasing 66% of the geologically based seismic moment along 12 km, or 24% of the total rupture length. Using our displacement distributions, we calculate kilometer-scale displacement gradients for the M7.1 rupture. The steepest gradients flank the 12-km-long region of maximum displacement and are ~13 m/km. In contrast, gradients for the 1992 M7.3 Landers and 1999 M7.1 Hector Mine earthquakes are <0.6 m/km. Our displacement distributions are important for understanding the influence of cross-fault rupture on M6.4 and M7.1 rupture length and displacement and will facilitate comparisons with distributions generated remotely and at broader scales.

      Assessment of continuous oil and gas resources in the Ordovician Collingwood Formation and Utica Shale of the Michigan Basin Province, 2019

      Released June 22, 2020 14:00 EST

      2020, Fact Sheet 2020-3027

      Christopher J. Schenk, Tracey J. Mercier, Cheryl A. Woodall, Heidi M. Leathers-Miller, Thomas M. Finn, Phuong A. Le, Michael E. Brownfield, Kristen R. Marra, Geoffrey S. Ellis

      Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean resources of 290 milllion barrels of shale oil and 7.9 trillion cubic feet of shale gas in the Ordovician Collingwood-Utica Shale Total Petroleum System of the Michigan Basin Province.

      Sample-size considerations for a study of shorebird nest survival in the 1002 Area, Arctic National Wildlife Refuge, Alaska

      Released June 22, 2020 12:30 EST

      2020, Open-File Report 2020-1066

      Emily L. Weiser

      Authorization of lease sales for oil development in the 1002 Area of the Arctic National Wildlife Refuge has highlighted gaps in information about biological communities in the area. The U.S. Fish and Wildlife Service, which is planning a study to evaluate spatial variation in the nest survival of tundra-breeding shorebirds to identify hotspots with high nest survival, sought advice from the U.S. Geological Survey on how to predict which sampling designs might be successful in achieving the study goals. I used previously obtained data on nest survival from Alaska’s North Slope to develop a simulation study that explored the statistical consequences of various sampling designs in the context of expected ranges of values of biological parameters. Of all sampling parameters, the number of nests per plot had the strongest influence on the ability to detect hotspots, followed by number of years of monitoring and the age at which nests were found. The benefit of sampling 98 plots instead of 68 was relatively small. Ages of nests cannot be predicted a priori, so I developed a field reference chart to identify when further nest-searching would be useful for a given plot. This simulation study used the best available information, but values of biological parameters will become better defined following subsequent data collection in the 1002 Area. Data from upcoming field seasons could be used to refine this analysis and improve estimation of the expected results of the field study, thus maximizing the likelihood that data from the 1002 Area nest survival study will meet the monitoring goals.

      Gas hydrates in sustainable chemistry

      Released June 22, 2020 09:22 EST

      2020, Chemical Society Reviews

      Aliakbar Hassanpouryouzband, Edris Joonaki, Mehrdad Vasheghani Farahania, Satoshi Takeya, Carolyn D. Ruppel, Jinhai Yang, Neill English, Judith Schicks, Katriona Edlmann, Hadi Mehrabian, Bahman Tohidi

      Gas hydrates have received considerable attention due to their important role in flow assurance for the oil and gas industry, their extensive natural occurrence on Earth and extraterrestrial planets, and their significant applications in sustainable technologies including but not limited to gas and energy storage, gas separation, and water desalination. Given not only their inherent structural flexibility depending on the type of guest gas molecules and formation conditions, but also the synthetic effects of a wide range of chemical additives on their properties, these variabilities could be exploited to optimise the role of gas hydrates. This includes increasing their industrial applications, understanding and utilising their role in Nature, identifying potential methods for safely extracting natural gases stored in naturally occurring hydrates within the Earth, and for developing green technologies. This review summarizes the different properties of gas hydrates as well as their formation and dissociation kinetics and then reviews the fast-growing literature reporting their role and applications in the aforementioned fields, mainly concentrating on advances during the last decade. Challenges, limitations, and future perspectives of each field are briefly discussed. The overall objective of this review is to provide readers with an extensive overview of gas hydrates that we hope will stimulate further work on this riveting field.

      Water-quality, bed-sediment, and invertebrate tissue trace-element concentrations for tributaries in the Clark Fork Basin, Montana, October 2017–September 2018

      Released June 22, 2020 07:18 EST

      2020, Open-File Report 2020-1067

      Gregory D. Clark, Michelle I. Hornberger, Thomas E. Cleasby, Terry L. Heinert, Matthew A. Turner

      Water, bed sediment, and invertebrate tissue were sampled in streams from Butte to near Missoula, Montana, as part of a monitoring program in the Clark Fork Basin. The sampling program was completed by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, to characterize aquatic resources in the Clark Fork Basin and monitor trace elements associated with historical mining and smelting activities. Sampling sites were on the river and tributaries of the Clark Fork. Water samples were collected periodically at 20 sites from October 2017 through September 2018. Bed-sediment and tissue samples were collected once at 13 sites during August 2018.

      Water-quality data included concentrations of major ions, dissolved organic carbon, nitrogen (nitrate plus nitrite), trace elements, and suspended sediment. Daily values of turbidity were determined at four sites. Bed-sediment data included trace-element concentrations in the fine-grained (less than 0.063 millimeter) fraction. Biological data included trace-element concentrations in whole-body tissue of aquatic benthic invertebrates. Statistical summaries of water-quality, bed-sediment, and invertebrate tissue trace element data for sites in the Clark Fork Basin were provided for the period of record: March 1985–September 2018.

      Sediment dynamics and implications for management: State of the science from long‐term research in the Chesapeake Bay watershed, USA

      Released June 21, 2020 10:06 EST

      2020, WIREs Water (4)

      Gregory B. Noe, Matthew J. Cashman, Katherine Skalak, Allen Gellis, Kristina G. Hopkins, Douglas Moyer, James Webber, Adam Benthem, Kelly O. Maloney, John Brakebill, Andrew Sekellick, Michael J. Langland, Qian Zhang, Gary Wynee Shenk, Jennifer L.D. Keisman, Cliff R. Hupp

      This review aims to synthesize the current knowledge of sediment dynamics using insights from long‐term research conducted in the watershed draining to the Chesapeake Bay, the largest estuary in the U.S., to inform management actions to restore the estuary and its watershed. The sediment dynamics of the Chesapeake are typical of many impaired watersheds and estuaries around the world, and this synthesis is intended to be relevant and transferable to other sediment‐impaired systems. The watershed's sediment sources, transport, delivery, and impacts are discussed with implications for effectively implementing best management practices (BMPs) to mitigate sediment issues. This synthesis revealed three key issues to consider when planning actions to reduce sediment loading: Scale, time, and land use. Geology and historical land use generated a template that current land use and climate, in addition to management, are acting upon to control sediment delivery. Important sediment sources in the Chesapeake include the Piedmont physiographic region, urban, and agricultural land use, and streambank erosion of headwater streams, whereas floodplain trapping is important along larger streams and rivers. Implementation of BMPs is widespread and is predicted to lead to decreased sediment loading; however, reworking of legacy sediment stored in stream valleys, with potentially long residence times in storage, can delay and complicate detection of the effects of BMPs on sediment loads. In conclusion, the improved understanding of sediment sources, storage areas, and transport lag times reviewed here can help target choices of BMP types and locations to better manage sediment problems—for both local streams and receiving waters.

      Effects of harmful algal blooms and associated water-quality on endangered Lost River and shortnose suckers

      Released June 20, 2020 10:17 EST

      2020, Harmful Algae (97)

      Summer M. Burdick, David A. Hewitt, Barbara A. Martin, Liam N. Schenk, Stewart Rounds

      Anthropogenic eutrophication contributes to harmful blooms of cyanobacteria in freshwater ecosystems worldwide. In Upper Klamath Lake, Oregon, massive blooms of Aphanizomenon flos-aquae and smaller blooms of other cyanobacteria are associated with cyanotoxins, hypoxia, high pH, high concentrations of ammonia, and potentially hypercapnia. Recovery of the endangered Lost River sucker Deltistes luxatus and shortnose sucker Chasmistes brevirostris in Upper Klamath Lake is obstructed by low survival in the juvenile life stage. Water quality associated with the harmful algal blooms and their decomposition (crashes) is often singled out as the primary cause of juvenile sucker mortality. We investigated this general hypothesis with a review of relevant literature and data from decades of monitoring in Upper Klamath Lake. Microcystins, hepatotoxins produced by some cyanobacteria, are unlikely to be directly lethal to suckers; potential effects of other cyanotoxins that are present in the lake warrant investigation. Dissolved-oxygen saturation declined following bloom crashes, but was infrequently low enough for long enough in Upper Klamath Lake to cause direct sucker mortality. Hypercapnia could potentially reach lethal concentrations in the fall and winter, but did not appear to be associated with the summer algal blooms. pH was highest during peaks in cyanobacteria growth, but infrequently reached directly lethal levels (> 10.3). However, pH frequently reached an observed sub-lethal effect level for juvenile suckers (10.0). Un-ionized ammonia rarely exceeded even the lowest effect level measured for suckers. Rather than act as a direct cause of large-scale mortality, the available evidence suggests that water quality associated with massive blooms of cyanobacteria in Upper Klamath Lake contributes to chronic stress for juvenile suckers and may increase mortality due to other factors.

      Envisioning a multi-agency and multi-academic institution geomorphology data exchange portal

      Released June 19, 2020 11:14 EST

      2020, Open-File Report 2020-1056

      Molly S. Wood, Paul M Boyd

      Access to bathymetry and geomorphology data for rivers and reservoirs is a critical need in multiple agencies and academia. These data are needed to make water-resource-management decisions regarding river restoration, resource protection, infrastructure design and sustainability, and flood-risk reduction, and during natural disasters. Sharing of data increases decision-making capacity by incorporating information from entire watersheds, provides knowledge from similar settings being managed or studied by other entities, and helps meet the goals of the Federal Open Water Data Initiative. Addressing these needs across broad spatial and temporal scales would be made more efficient if these data were available in consistent formats with standardized metadata and were either stored in a centralized database or integrated with existing geospatial datasets. Because of renewed interest and technological advances, representatives from multiple Federal agencies and academic institutions have created a new working group to scope the development of a Geomorphology Data Exchange Portal to increase access to needed data. The working group has developed a vision for the Portal and outlined possible approaches to achieve the vision. Short-term approaches may include leveraging existing data-access portals and data-processing tools and integrating geomorphology data with existing national geospatial datasets.

      Hurricane Sandy effects on coastal marsh elevation change

      Released June 19, 2020 09:19 EST

      2020, Estuaries and Coasts

      Alice G. Yeates, James Grace, Jennifer H. Olker, Glenn R. Guntenspergen, Donald Cahoon, Susan C. Adamowicz, Shimon C. Anisfeld, Nels Barrett, Alice Benzecry, Linda K. Blum, Rober T Christian, Joseph Grzyb, Ellen Kracauer Hartig, Kelly Hines Leo, Scott Lerberg, James C. Lynch, Nicole Maher, J Patrick Megonigal, William G. Reay, Drexel Siok, Adam Starke, Vincent Turner, Scott Warren

      High-magnitude storm events such as Hurricane Sandy are powerful agents of geomorphic change in coastal marshes, potentially altering their surface elevation trajectories. But how do a storm’s impacts vary across a large region spanning a variety of wetland settings and storm exposures and intensities. We determined the short-term impacts of Hurricane Sandy at 223 surface elevation table–marker horizon stations in estuarine marshes located across the northeast region of the United States by comparing post-storm surface elevation change with pre-storm elevation trends. We hypothesized that the storm’s effect on marsh elevation trends would be influenced by position relative to landfall (right or left) and distance from landfall. The structural equation model presented predicts that marshes located to the left of landfall were more likely to experience an elevation gain greater than expected, and this positive deviation from pre-storm elevation trends tended to have a greater magnitude than those experiencing negative deviations (elevation loss), potentially due to greater sediment deposition. The magnitude of negative deviations from elevation change in marshes to the right of landfall was greater than for positive deviations, with a greater effect in marshes within 200 km of landfall, potentially from the extent and magnitude of storm surge. Overall, results provide an integrated picture of how storm characteristics combined with the local wetland setting are important to a storm’s impact on surface elevation, and that the surface elevation response can vary widely among sites across a region impacted by the same storm.

      The effects of management practices on grassland birds—Baird’s Sparrow (Centronyx bairdii)

      Released June 18, 2020 16:00 EST

      2020, Professional Paper 1842-HH

      Jill A. Shaffer, Lawrence D. Igl, Douglas H. Johnson, Marriah L. Sondreal, Christopher M. Goldade, Melvin P. Nenneman, Betty R. Euliss

      Keys to Baird’s Sparrow (Centronyx bairdii) management are providing native or tame grasslands with moderately deep litter, controlling excessive grazing, and curtailing shrub encroachment. Baird’s Sparrows have been reported to use habitats with less than or equal to (≤) 101 centimeters (cm) average vegetation height, 3–46 cm visual obstruction reading (VOR), 15–71 percent grass cover, 5–25 percent forb cover, ≤50 percent shrub cover, less than (<) 44 percent bare ground, 10–63 percent litter cover, and ≤21 cm litter depth.

      Structural impacts, carbon losses, and regeneration in mangrove wetlands after two hurricanes on St. John, U.S. Virgin Islands

      Released June 18, 2020 08:59 EST

      2020, Wetlands

      Ken Krauss, Andrew From, Caroline Rogers, Kevin R.T. Whelan, Kristen W. Grimes, Robert C. Dobbs, Thomas Kelley

      Hurricanes Irma and Maria ravaged the mangroves of St. John, U.S. Virgin Islands, in 2017. Basal area losses were large (63–100%) and storm losses of carbon associated with aboveground biomass amounted to 11.9–43.5 Mg C/ha. Carbon biomass of dead standing trees increased 8.1–18.3 Mg C/ha among sites, and carbon in coarse woody debris on the forest floor increased 1.9–18.2 Mg C/ha, with effects varying by mangrove typology. While St. John has only ~45 ha of mangroves, they exist as isolated basins, salt ponds, and fringe mangroves; the latter sometimes support diverse marine communities. Salt pond and fringe mangroves had proportionately more organic carbon (46.3 Mg C/ha) than inorganic carbon (1.1 Mg C/ha) in soils than isolated basins. Soil organic carbon was also appreciable in isolated basins (30.8 Mg C/ha) but was matched by inorganic C (36.7 Mg C/ha), possibly due to adjacent land use history (e.g., road construction), previous storm overwash, or geomorphology. Soil nitrogen stocks were low across all typologies. Mangroves had limited regeneration 26 months after the storms, and recovery on St. John may be hindered by pre-storm hydrologic change in some stands, and potential genetic bottlenecks and lack of propagule sources for expedient recovery in all stands.

      Modeling Escherichia coli in the Missouri River near Omaha, Nebraska, 2012–16

      Released June 17, 2020 15:15 EST

      2020, Scientific Investigations Report 2020-5045

      Brenda K. Densmore, Brent M. Hall, Matthew T. Moser

      The city of Omaha, Nebraska, has a combined sewer system in some areas of the city. In Omaha, Nebr., a moderate amount of rainfall will lead to the combination of stormwater and untreated sewage or wastewater being discharged directly into the Missouri River and Papillion Creek and is called a combined sewer overflow (CSO) event. In 2009, the city of Omaha began the implementation of their Long Term Control Plan (LTCP) to mitigate the effects of CSOs on the Missouri River and Papillion Creek. As part of the LTCP, the city partnered with the U.S. Geological Survey (USGS) in 2012 to begin monitoring in the Missouri River. Since 2012, monthly discrete water-quality samples for many constituents have been collected from the Missouri River at four sites. At 3 of the 4 sites, water quality has been monitored continuously for selected constituents and physical properties. These discrete water-quality samples and continuous water-quality monitoring data (from July 2012 to 2020) have been collected to better understand the water quality of the Missouri River, how it is changing with time, how it changes upstream from the city of Omaha to downstream, and how it varies during base-flow conditions and during periods of runoff.

      The purpose of this report is to document the development of Escherichia coli (E. coli) concentration models for these four Missouri River sites. Analysis was completed using the first 5 years of data (through 2016) to determine if the current approach is sufficient to meet future analysis goals and to understand if proposed models such as Load Estimator (LOADEST) models will be able to represent water-quality changes in the Missouri River.

      Multiple linear regression models were developed to estimate E. coli concentration using LOADEST as implemented in the rloadest package in the R statistical software program. A set of explanatory variables, including streamflow and streamflow anomalies, precipitation, information about CSOs, and continuous water quality, were evaluated for potential inclusion in regression models. The best model at Missouri River at NP Dodge Park at Omaha, Nebr. (USGS station 412126095565201; hereafter “NP Dodge”) included basin explanatory variables of upstream antecedent precipitation index measured at Tekamah, Nebr.; decimal time; season; and turbidity. The best model at Missouri River at Freedom Park Omaha, Nebr. (USGS station 411636095535401; hereafter “Freedom Park”) included the same explanatory variables as the NP Dodge model with the addition of turbidity anomalies and flow anomalies. The best models at the two downstream sites (Missouri River near Council Bluffs, Iowa, USGS station 06610505 and Missouri River near La Platte, Nebr., USGS station 410333095530101) included the same explanatory variables as the Freedom Park model with the addition of local antecedent precipitation index as measured at Eppley Airport in Omaha, Nebr., and additional turbidity and flow anomalies. The final selected models were the best models given our modeling design constraint in which explanatory variables included in the model for the upstream site were included in the downstream models.

      Explanatory variables currently (2020) being collected and included in the selected models through 2016 explained 64–75 percent of the variability of E. coli concentration in the Missouri River. Explaining 64–75 percent of the variability might be considered low when working with physical constituents (total nitrogen or sediment), but with the natural variability of biological constituents such as E. coli, the uncertainty of E. coli laboratory measurements, and the added complexity of modeling in a large drainage basin with multiple sources, these results are adequate and indicate that the explanatory variables being collected and models such as LOADEST can represent water-quality changes in the Missouri River for E. coli concentration from 2012 to 2016.

      Comparing trends in modeled and observed streamflows at minimally altered basins in the United States

      Released June 17, 2020 09:43 EST

      2020, Water (12)

      Glenn A. Hodgkins, Robert Dudley, Amy M. Russell, Jacob H. LaFontaine

      We compared modeled and observed streamflow trends from 1984–2016 using five statistical transfer models and one deterministic, distributed-parameter, process-based model, for 26 flow metrics at 502 basins in the United States that are minimally influenced by development. We also looked at a measure of overall model fit and average bias. A higher percentage of basins, for all models, had relatively low trend differences between modeled and observed mean/ median flows than for very high or low flows such as the annual 1-day high and 7-day low flows. Mean-flow metrics also had the largest percentage of basins with relatively good overall model fit and low bias. The five statistical transfer models performed better at more basins than the process-based model. The overall model fit for all models, for mean and/or high flows, was correlated with one or more measures of basin precipitation or aridity. Our study and previous studies generally observed good model performance for high flows up to 90th or 95th percentile flows. However, we found model performance was substantially worse for more extreme flows, including 99th percentile and annual 1-day high flows; this shows the importance of including more extreme high flows in analyses of model performance.

      Small basin annual yield and percentage of snowmelt runoff in North Dakota, 1931–2016

      Released June 17, 2020 07:36 EST

      2020, Scientific Investigations Report 2019-5144

      Tara Williams-Sether, Spencer L. Wheeling

      The North Dakota hydrology manual prepared by the U.S. Department of Agriculture, Soil Conservation Service, presents methodologies primarily used for developing hydrology for onfarm conservation practices, watershed projects, Resource Conservation and Development project measures, and river basin studies. The manual includes data necessary for determining hydrologic factors and developing a design discharge for a given site and intended purpose. The U.S. Geological Survey, in cooperation with the North Dakota Natural Resources Conservation Service, developed methods to reproduce and update the annual yield maps for chapter 7 of the North Dakota hydrology manual. Annual yields, in acre-feet per square mile, for the 50- and 80-percent exceedance probabilities and expected percentage of snowmelt runoff isolines were estimated using U.S. Geological Survey streamflow data from 1931 to 2016 for 71 selected streamgages with drainage areas of 505 square miles or less. An application of a modified Maintenance of Variance Extension Type III was used to estimate missing annual streamflow volumes. An alternate expected percentage of snowmelt runoff isolines was estimated using High Plains Climatic Center precipitation and snowmelt data from 1931 to 2016 for 85 selected sites. The final expected percentage of snowmelt runoff isolines was estimated using streamflow data instead of precipitation and snowfall depth data. A snowmelt runoff seasonal period of March–May produced better isoline slopes than a November–May runoff seasonal period. Slopes of the expected percentage of snowmelt runoff isolines were sensitive to amounts of missing record. Suitable isoline slopes appeared when the missing record was set to 50 percent (43 years) and 66 percent (57 years) for the 86-year period of 1931–2016.

      Missouri StreamStats—St. Louis County and the City of St. Louis urban application

      Released June 16, 2020 09:37 EST

      2020, Scientific Investigations Report 2020-5040

      Rodney E. Southard, Tana Haluska, Joseph M. Richards, Jarrett T. Ellis, Christine Dartiguenave, Dean Djokic

      To address a major limitation of the functionality of the Missouri statewide StreamStats application in the urban areas of St. Louis County and the City of St. Louis, Missouri, the U.S. Geological Survey, in cooperation with the Metropolitan St. Louis Sewer District, defined watershed boundaries and hydrography for the study area using high-resolution 3-meter digital elevation data derived from light detection and ranging sources, high-resolution 6-inch imagery, and storm sewer network geospatial data. The combined sanitary sewers, a part of the storm sewer network, were integrated into the open channel hydrography and elevation data using a new Arc Hydro stormwater tool developed to facilitate the incorporation of the combined sanitary sewer network into the StreamStats application.

      The combined sanitary sewer network was edited for connectivity and flow direction before integration into the Missouri-St. Louis StreamStats application. Inlet structures in the geospatial data were defined as HydroJunction features that allow for stormwater runoff to enter the combined sanitary sewer network. An Arc Hydro stormwater processing workflow and a sewershed delineation tool were developed to integrate the combined sanitary sewer network with the hydrographic dataset and digital elevation model in the study area.

      The StreamStats application developed for the study area provides various data exploration tools that can be used to examine the spatial data and to obtain general descriptive information and flow statistics at streamgages in the study area. Watersheds and sewersheds can be delineated and basin characteristics can be determined at any point on the open channel network or the combined sanitary sewer network in the study area. Peak-flow statistics can be computed at any point on the open channel network. A report summarizing the results is generated by the StreamStats application and can be downloaded and used in other software.

      The Missouri-St. Louis StreamStats application is limited to the area inside St. Louis County and the City of St. Louis and excludes locations on the main stem of the Mississippi, Missouri, and Meramec Rivers. The limitations of the Missouri-St. Louis StreamStats application include possible inaccuracies using regression equations for peak-flow statistics developed assuming natural flow conditions and topographically derived watersheds determined from a coarser resolution of data than is used in this application. Additionally, published regression equations for peak-flow statistics did not incorporate any pipe flow or sewershed delineations when they were developed, which limits the applicability of peak-flow statistics to basins based on primarily topographic delineation. Inaccuracies in resolution, completeness, location, or attribution of geospatial elevation data, hydrographic data, derived stream lines, derived watershed boundaries, and combined sanitary sewer data can limit the accuracy and functionality of the Missouri-St. Louis StreamStats application.

      Conceptual framework and approach for conducting a geoenvironmental assessment of undiscovered uranium resources

      Released June 16, 2020 09:20 EST

      2020, Scientific Investigations Report 2018-5104

      Tanya J. Gallegos, Katherine Walton-Day, Robert R. Seal II

      This report presents a novel conceptual framework and approach for conducting a geologically based environmental assessment, or geoenvironmental assessment, of undiscovered uranium resources within an area likely to contain uranium deposits. The framework is based on a source-to-receptor model that prioritizes the most likely contaminant sources, contaminant pathways, and affected environmental media for three common uranium extraction methods—open pit or underground mining with milling and in situ recovery (ISR). Data on regional geology, hydrology, and climate, as well as historical uranium mining and milling records are used to estimate the probable amounts of waste rock, tailings, wastewater, surface land disturbance, and subsurface aquifer disturbance for likely mining methods. Constituents of concern that might take the form of leachates, dust, radon, and sediments formed by chemical and physical weathering are also identified in the geoenvironmental assessment. Finally, areas where constituents of concern are likely to occur and persist in air, land, surface water, and groundwater are indicated by the potential for dispersion of dust by wind, accumulation of radon because of air stagnation, dispersion of sediments and wastewater by runoff, and infiltration of wastewater or leachates with consideration of the likely mobility of contaminants in surface water and groundwater. The geoenvironmental assessment output can be summarized in the following primary products: (1) a descriptive geoenvironmental model; (2) maps and statistics of variables that indicate the potential for constituents of concern to occur and persist in air, land, surface water, and groundwater within a tract that is geologically permissive for the occurrence of uranium; and (3) tables providing estimated or indicated quantities of waste rock, tailings, wastewater, dust, and radon emissions that could be associated with undiscovered uranium resources, if extracted, for each permissive tract. The uranium geoenvironmental assessment could help natural resource managers to prioritize and (or) identify (1) important potential contaminant pathways, (2) management practices required depending on the types of constituents that could be of concern, (3) areas for response in the event of accidental release, and (4) future directions for study. Furthermore, indicators of rock and water volumes potentially associated with an undiscovered uranium deposit may be evaluated to make quantitative comparisons of water required for uranium production or potential waste products generated during uranium extraction from areas permissive for uranium resource occurrence throughout the United States.

      Updating data inputs, assessing trends, and evaluating a method to estimate probable high groundwater levels in selected areas of Massachusetts

      Released June 15, 2020 10:50 EST

      2020, Scientific Investigations Report 2020-5036

      Janet R. Barclay, John R. Mullaney

      A method to estimate the probable high groundwater level in Massachusetts, excluding Cape Cod and the islands, was developed in 1981. The method uses a groundwater measurement from a test site, groundwater measurements from an index well, and a distribution of high groundwater levels from wells in similar geologic and topographic settings. The U.S. Geological Survey, in cooperation with the Massachusetts Department of Environmental Protection, conducted an update to the Frimpter method for estimating the probable high groundwater levels in Massachusetts. The study evaluated the potential changes to the method resulting from four decades of additional groundwater-level data and the expansion of the network of wells for monitoring groundwater levels. The differences and potential benefits of daily, as opposed to monthly, measurements in the application of the method were examined because of the increased availability of high-frequency (subdaily) groundwater-level data. The study also considered long-term trends in groundwater levels that may alter the accuracy of the method. Finally, the accuracy of the estimated high groundwater levels was evaluated, and improved implementation guidance was prepared.

      For this study, groundwater levels in 153 wells in Massachusetts and surrounding States with records with lengths of 16 to 78 years were analyzed. The highest recorded groundwater levels ranged from 1.2 feet (ft) above land surface (flooded conditions) to 45.8 ft below land surface, with a median of 4.6 ft below land surface. The maximum annual groundwater-level range was 1.4 to 17.9 ft, with a median of 5.5 ft.

      The within-month variation, maximum annual groundwater-level range, and highest recorded groundwater level were computed using daily mean groundwater-level values from 28 wells with continuous records. The use of daily data resulted in larger maximum annual groundwater-level ranges (0.02 to 2.94 ft larger, with a median of 0.58 ft larger) and shallower highest-recorded groundwater levels (0.0 to 1.60 ft shallower, with a median of 0.18 ft shallower) than computations based on monthly measurements in the same wells.

      Statistical tests showed moderate to strong evidence of trends in measurements of both high and low groundwater levels within most of the periods during which water levels were analyzed. High groundwater levels rose beneath the land surface at most sites during four of the six periods used for analysis (1966–2015, 1986–2015, 1991–2010, and 1981–2010). Low groundwater levels also increased at many sites during most of the periods evaluated, but this trend was less widespread than the similar trends in high groundwater levels, and the trend was to deeper low groundwater levels at more sites than the trend to deeper high groundwater levels. There was no clear trend in annual groundwater-level ranges at most sites during the six periods analyzed.

      In general, the Frimpter method predicted shallower (higher) high groundwater levels than were observed but correctly classified sites according to their suitabilities for unmounded septic systems. The mean error of the predictions (difference between the estimated and observed groundwater levels) ranged from −3.23 ft to −1.40 ft for various approaches to estimating the groundwater-level range and selecting an index well. The method correctly classified 83 to 86 percent of monitoring-well sites according to their suitability for an unmounded septic system for many approaches to estimating the annual groundwater-level range and selecting an index well. The approach selected for estimating the annual groundwater-level range and selecting an index well will depend upon the importance of an accurate estimate of the high groundwater level as compared to the importance of an estimated high groundwater level that is less likely to be exceeded.

      Dietary fat concentrations influence fatty acid assimilation patterns in Atlantic pollock (Pollachius virens)

      Released June 15, 2020 09:56 EST

      2020, Philosophical Transactions of the Royal Society B: Biological Sciences (375)

      Suzanne M. Budge, Katherine Townsend, Santosh P Lall, Jeffrey F. Bromaghin

      A key aspect in the use of fatty acids (FA) to estimate predator diets using Quantitative FA Signature Analysis (QFASA) is the ability to account for FA assimilation through the use of calibration coefficients (CC). Here, we tested the assumption that CC are independent of dietary fat concentrations by feeding Atlantic pollock (Pollachius virens) three formulated diets with very similar FA proportions but different fat concentrations (5 – 9 % of diet) for 20 weeks. CC calculated using FA profiles of diet and triacylglycerols in pollock liver were significantly different for the three diets. To test the robustness of diet estimates to these differences, we used the CC set derived from feeding the diet with the lowest fat concentration, published prey FA profiles and realistic diet estimates of pollock to construct ‘pseudo-predators’. Application of QFASA to each pseudo-predator using the three sets of CC and the same prey FA profiles resulted in diet estimate biases of 2-fold for major prey items and ~ 5-fold for minor prey items. This work illustrates the importance of incorporating diets with fat concentrations that are similar to natural prey when conducting feeding experiments to calculate CC.

      Snow processes in mountain forests: Interception modeling for coarse-scale applications

      Released June 15, 2020 09:50 EST

      2020, Hydrology and Earth System Sciences (24) 2545-2560

      N. Helbig, C. David Moeser, M. Teich, L. Vincent, Y. Lejeune, J.-E. Sicart, J.-M. Monnet

      Snow interception by the forest canopy controls the spatial heterogeneity of subcanopy snow accumulation leading to significant differences between forested and nonforested areas at a variety of scales. Snow intercepted by the forest canopy can also drastically change the surface albedo. As such, accurately modeling snow interception is of importance for various model applications such as hydrological, weather, and climate predictions. Due to difficulties in the direct measurements of snow interception, previous empirical snow interception models were developed at just the point scale. The lack of spatially extensive data sets has hindered the validation of snow interception models in different snow climates, forest types, and at various spatial scales and has reduced the accurate representation of snow interception in coarse-scale models. We present two novel empirical models for the spatial mean and one for the standard deviation of snow interception derived from an extensive snow interception data set collected in an evergreen coniferous forest in the Swiss Alps. Besides open-site snowfall, subgrid model input parameters include the standard deviation of the DSM (digital surface model) and/or the sky view factor, both of which can be easily precomputed. Validation of both models was performed with snow interception data sets acquired in geographically different locations under disparate weather conditions. Snow interception data sets from the Rocky Mountains, US, and the French Alps compared well to the modeled snow interception with a normalized root mean square error (NRMSE) for the spatial mean of ≤10 % for both models and NRMSE of the standard deviation of ≤13 %. Compared to a previous model for the spatial mean interception of snow water equivalent, the presented models show improved model performances. Our results indicate that the proposed snow interception models can be applied in coarse land surface model grid cells provided that a sufficiently fine-scale DSM is available to derive subgrid forest parameters.

      Baseline conditions and projected future hydro-climatic change in National Parks in the conterminous United States

      Released June 15, 2020 08:24 EST

      2020, Water (6)

      William A. Battaglin, Lauren Hay, David J. Lawrence, Gregory J. McCabe, Parker A. Norton

      The National Park Service (NPS) manages hundreds of parks in the United States, and many contain important aquatic ecosystems and/or threatened and endangered aquatic species vulnerable to hydro-climatic change. Effective management of park resources under future hydro-climatic uncertainty requires information on both baseline conditions and the range of projected future conditions. A monthly water balance model was used to assess baseline (1981-1999) conditions and a range of projected future hydro-climatic conditions in 374 NPS parks. General circulation model outputs representing 214 future climate simulations were used to drive the model. Projected future changes in temperature (T), precipitation (P), and runoff (R) are expressed as departures from historical baselines. Climate simulations indicate increasing T in 2030 for all parks with 50th percentile simulations projecting increases of 1.67 oC or more in 50% of parks. Departures in 2030 P indicate a mix of mostly increases and some decreases, with 50th percentile simulations projecting increases in P in more than 70% of parks. Departures in R for 2030 are mostly decreases , with the 50th percentile simulations projecting decreases in R in more than 50% of parks in all seasons except winter. Hence in many parks, R is projected to decrease even when P is projected to increase because of increasing T in all NPS parks. Projected changes in future hydro-climatic conditions can also be assessed for individual parks, and Rocky Mountain National Park and Congaree National Park are used as examples.

      Annual adult survival drives trends in Arctic-breeding shorebirds but knowledge gaps in other vital rates remain

      Released June 13, 2020 09:25 EST

      2020, The Condor (1222)

      Emily L. Weiser, Richard B. Lanctot, Stephen C. Brown, H. River Gates, Joel Bety, Megan L. Boldenow, Rodney W. Brook, Glen S. Brown, Willow B. English, Scott A. Flemming, Samantha E. Franks, H. Grant Gilchrist, Marie-Andree Giroux, Andrew Johnson, Steve Kendall, Lisa V. Kennedy, Laura Koloski, Eunbi Kwon, Jean-Francois Lamarre, David B. Lank, Christopher J. Latty, Nicolas Lecomte, Joseph R. Liebezeit, Rebecca L McGuire, Laura McKinnon, Erica Nol, David C. Payer, Johanna Perz, Jennie Rausch, Martin D. Robards, Sarah T. Saalfeld, Nathan R. Senner, Paul A. Smith, Mikhail Soloviev, Diana V Solovyeva, David H. Ward, Paul F. Woodard, Brett K. Sandercock

      Conservation status and management priorities are often informed by population trends. Trend estimates can be derived from population surveys or models, but both methods are associated with sources of uncertainty. Many Arctic-breeding shorebirds are thought to be declining based on migration and/or overwintering population surveys, but data are lacking to estimate the trends of some shorebird species. In addition, for most species, little is known about the stage(s) at which population bottlenecks occur, such as breeding vs. nonbreeding periods. We used previously published and unpublished estimates of vital rates to develop the first large-scale population models for 6 species of Arctic-breeding shorebirds in North America, including separate estimates for 3 subspecies of Dunlin. We used the models to estimate population trends and identify life stages at which population growth may be limited. Our model for the arcticola subspecies of Dunlin agreed with previously published information that the subspecies is severely declining. Our results also linked the decline to the subspecies’ low annual survival rate, thus potentially implicating factors during the nonbreeding period in the East Asian-Australasian Flyway. However, our trend estimates for all species showed high uncertainty, highlighting the need for more accurate and precise estimates of vital rates. Of the vital rates, annual survival had the strongest influence on population trend in all taxa. Improving the accuracy, precision, and spatial and temporal coverage of estimates of vital rates, especially annual survival, would improve demographic model-based estimates of population trends and help direct management to regions or seasons where birds are subject to higher mortality.

      DOI/GTN-P climate and active-layer data acquired in the National Petroleum Reserve–Alaska and the Arctic National Wildlife Refuge, 1998–2016

      Released June 12, 2020 16:00 EST

      2018, Data Series 1092

      Frank E. Urban, Gary D. Clow

      This report provides data collected by the climate monitoring array of the U.S. Department of the Interior on Federal lands in Arctic Alaska over the period August 1998 to July 2017; this array is part of the Global Terrestrial Network for Permafrost (DOI/GTN-P). In addition to presenting data, this report also describes monitoring, data collection, and quality-control methods. The array of 16 monitoring stations spans lat 68.5°N. to 70.5°N. and long 142.5°W. to 161°W., an area of approximately 150,000 square kilometers. Climate summaries are presented along with quality-controlled data. Data collection is ongoing and includes the following climate- and permafrost-related variables: air temperature, wind speed and direction, ground temperature, soil moisture, snow depth, rainfall totals, up- and downwelling shortwave radiation, and atmospheric pressure. These data were collected by the U.S. Geological Survey in close collaboration with the Bureau of Land Management and the U.S. Fish and Wildlife Service.

      Regional patterns in hydrologic response, a new three-component metric for hydrograph analysis and implications for ecohydrology, Northwest Volcanic Aquifer Study Area, USA

      Released June 12, 2020 09:48 EST

      2020, Journal of Hydrology: Regional Studies (30)

      Jennifer A. Curtis, Erick Burns, Roy Sando

      Study Region

      Oregon, California, Idaho, Nevada and Utah

      Study Focus

      Spatial patterns of hydrologic response were examined for the Northwest Volcanic Aquifer Study Area (NVASA). The utility of established hydrograph-separation methods for assessing hydrologic response in permeable volcanic terranes was assessed and a new three-component metric for hydrograph analysis was developed. The new metric, which partitions streamflow into subcomponents defined by the timescales of hydrologic response (e.g., fast-runoff, intermediate-interflow and slow-baseflow), was used to gain a fundamental understanding of the regional hydrology, investigate sub-regional differences, influencing factors, and ecohydrological implications.

      New Hydrological Insights

      The combined effects of NVASA’s physiography, climate and geology create a strongly coupled surface-groundwater system that produces copious baseflow and limited quantities of runoff and interflow. Patterns of hydrologic response are influenced by the type and rate of precipitation and permeability of the underlying geology. Under variable precipitation conditions the hydrologic response of volcanic terranes with similar permeability and subsurface-storage capacity can be significantly different. From a water management and ecohydrology perspective, understanding regional patterns of hydrologic response and sub-regional differences is fundamental. Results indicate that minimum-flow methods provide the most conservative estimate of baseflow and may be the most robust for filtering out snowmelt bias in baseflow estimates. Baseflow contributes ∼75% of the perennial streamflow across the NVASA and represents a critical component of the regional water supply that provides critical cold-water habitat.

      Statewide assessment of karst aquifers in New York with an inventory of closed-depression and focused-recharge features

      Released June 12, 2020 09:45 EST

      2020, Scientific Investigations Report 2020-5030

      William M. Kappel, James E. Reddy, Jonathan C. Root

      Karst is a landscape formed from the dissolution of soluble rock or rock containing minerals that are easily dissolved from within the rock. The landscape is characterized by sinkholes, caves, losing streams, springs, and underground drainage systems, which rapidly move water through the karst. The two forms of karst in New York State include carbonate karst, which forms in carbonate rock (limestone, marble, and dolostone), and evaporite karst, which forms in rock that contains the evaporite minerals gypsum and halite.

      Past and recent studies of karst across the State have shown that areas of focused recharge in karstic carbonate rock allow contaminants to enter aquifer systems with little attenuation. Focused areas of recharge need to be identified to help prevent such contamination from sources on or adjacent to the karst. The New York State Departments of Environmental Conservation and Health are collaborating with the agricultural community to make farmers and farm-planning advisors more aware of karst and how to manage daily farming activities to reduce their impact on surface water and groundwater resources, especially in karst areas. There is also a need to make regulators, planners, and the general public aware of New York’s karst resources and to properly protect and manage these resources to protect the quality of groundwater and surface water that can flow into, through, and from karst bedrock.

      Using publicly available geospatial data, karst bedrock and closed depressions over or near karst rock were identified across New York. Carbonate, evaporite, and marble geologic units were selected from a statewide 1:250,000-scale bedrock geology dataset. The selected geologic units were intersected with 7.5-minute quadrangle maps to define the study area.

      The U.S. Geological Survey has compiled an inventory of closed depressions from statewide digital contour data, scanned 7.5-minute topographic maps known as a digital raster graphics, and light detection and ranging (lidar) digital elevation models. Analysis of the data resulted in the identification of 5,023 closed depressions statewide. The inventory was conducted to eliminate duplication of results from analysis of the three data sources. A series of overlay analyses was conducted using the closed depressions and thematic data known to be key factors in determining the probability of a closed depression contributing to focused groundwater recharge; the thematic data include bedrock geology, soil type, soil infiltration rate, and land cover.

      Though the extent of karst development is important in understanding the interaction between surface water and groundwater in karst terrains, some of the worst cases of groundwater contamination in karst can occur where only minor karst features might be present. The presence of karst—be it a short section of a solutioned fracture or an extensive cave system—requires careful consideration, forward-looking environmental planning, and consistent water-quality protection to preserve New York State’s water resources.

      Selected geologic maps of the Kodiak batholith and other Paleocene intrusive rocks, Kodiak Island, Alaska

      Released June 12, 2020 07:52 EST

      2020, Scientific Investigations Map 3441

      David W. Farris, Peter J. Haeussler

      Kodiak Island in southern Alaska is one of the premier examples globally for the study of forearc magmatism. This location contains two Paleocene intrusive belts that formed due to the subduction of a migrating spreading ridge and slab-window: the Kodiak batholith and the trenchward magmatic belt. These magmatic rocks are part of the Sanak-Baranof belt, which extends for greater than 2,100 km along the southern Alaskan margin and vary in age from 61 to 50 Ma west to east.

      Trenchward-belt rocks, with an 40Ar/39Ar age of 60.2±0.9 Ma, intrude into the Paleocene Ghost Rocks Formation and are composed of granitoids, basaltic dikes, and small gabbroic plutons that lie along or southward of the Kalsin Bay Fault. Such intrusions were emplaced at shallow levels and have abundant evidence of incomplete intermingling of basaltic and granitic magmas. These textures indicate trenchward-belt intrusions that froze before complete assimilation, leaving behind features such as abundant locally stoped blocks, gabbroic pods within granitic intrusions, and microstructural evidence such as strongly embayed olivine and pyroxene phenocrysts in granitoid bodies.

      The Kodiak batholith and satellite intrusions extend for over 110 km along the axis of Kodiak Island and vary in width from 2 to 6 km. These intrude into the Late Cretaceous Kodiak Formation. U-Pb ages on zircon from the intrusions range from 59.2±0.2 Ma in the southwest to 58.4±0.2 Ma near its northwest tip. We interpret these ages as tracking the location of a migrating triple junction and associated slab-window. The batholith is composed of granite and granodiorite, with lesser amounts of tonalite and diorite. The center of the Kodiak batholith contains high-inclusion zones with abundant residual host rock fragments that were carried up from 5–10 km below current exposure levels. These high-inclusion zones contain biotite aggregates, pure quartz clots, and large xenocrysts of sillimanite, kyanite, andalusite, and garnet. This is a higher-pressure mineral assemblage than exists in the batholith metamorphic aureole. Gravity observations and modeling are consistent with the high-inclusion zones extending downward for 5–10 km. The Kodiak batholith results from a migrating triple junction and slab-window that led to high degrees of partial melting within the Kodiak accretionary prism.

      Increased drought severity tracks warming in the United States’ largest river basin

      Released June 11, 2020 13:03 EST

      2020, PNAS (117) 11328-11336

      Justin Martin, Gregory T. Pederson, Connie A. Woodhouse, Edward R. Cook, Gregory J. McCabe, Kevin J. Anchukaitis, Erika K. Wise, Patrick Erger, Larry S. Dolan, Marketa McGuire, Subhrendu Gangopadhyay, Katherine J. Chase, Jeremy S. Littell, Stephen Gray, Scott St. George, Jonathan M. Friedman, David J. Sauchyn, Jeannine-Marie St. Jacques, John C. King

      Across the Upper Missouri River Basin, the recent drought of 2000 to 2010, known as the “turn-of-the-century drought,” was likely more severe than any in the instrumental record including the Dust Bowl drought. However, until now, adequate proxy records needed to better understand this event with regard to long-term variability have been lacking. Here we examine 1,200 y of streamflow from a network of 17 new tree-ring–based reconstructions for gages across the upper Missouri basin and an independent reconstruction of warm-season regional temperature in order to place the recent drought in a long-term climate context. We find that temperature has increasingly influenced the severity of drought events by decreasing runoff efficiency in the basin since the late 20th century (1980s) onward. The occurrence of extreme heat, higher evapotranspiration, and associated low-flow conditions across the basin has increased substantially over the 20th and 21st centuries, and recent warming aligns with increasing drought severities that rival or exceed any estimated over the last 12 centuries. Future warming is anticipated to cause increasingly severe droughts by enhancing water deficits that could prove challenging for water management.

      Juvenile Lost River and shortnose sucker year-class formation, survival, and growth in Upper Klamath Lake, Oregon, and Clear Lake Reservoir, California—2018 monitoring report

      Released June 11, 2020 13:00 EST

      2020, Open-File Report 2020-1064

      Ryan J. Bart, Summer M. Burdick, Marshal S. Hoy, Carl O. Ostberg

      Executive Summary

      Populations of federally endangered Lost River (Deltistes luxatus) and shortnose suckers (Chasmistes brevirostris) in Upper Klamath Lake, Oregon, and Clear Lake Reservoir (hereinafter Clear Lake), California, are experiencing long-term decreases in abundance. Upper Klamath Lake populations are decreasing not only because of adult mortality, which is relatively low, but also because they are not being balanced by recruitment of young adult suckers into known adult spawning aggregations.

      Long-term monitoring of juvenile sucker populations is conducted to (1) determine if there are annual and species-specific differences in production, survival, and growth; (2) better understand when juvenile sucker mortality is greatest, and (3) help identify potential causes of high juvenile sucker mortality, particularly in Upper Klamath Lake. The U.S. Geological Survey monitoring program, which began in 2015, tracks cohorts through summer months and among years in Upper Klamath and Clear Lakes. Data on juvenile suckers captured in trap nets are used to provide information on annual variability in age-0 sucker apparent production, juvenile sucker apparent survival, apparent growth, species composition, and health.

      Juvenile sucker year-class strength and apparent survival were low in 2018 in Upper Klamath Lake. Most juvenile sucker mortality occurs within the first year of life. The Upper Klamath Lake year-class strength indices for Lost River and shortnose suckers in 2018 were the lowest they had been since the start of monitoring in 2015. The annual catch rates of shortnose sucker remained consistently low, whereas Lost River sucker catch rates varied. The capture of only four age-1 and older suckers from Upper Klamath Lake during the 2018 sampling season indicated low annual survival of the 2017 cohort.

      Annual production indices of juvenile suckers in Clear Lake are highly variable and potentially affected by seasonal connections to spawning habitat in Willow Creek. A total of seven age-0 shortnose or Klamath largescale suckers (Catostomus snyderi) were captured from Clear Lake in 2018, which was a relatively wet year, indicating that a small cohort was formed or that there was a delay in the recruitment of age-0 suckers. The 2018 sampling continued to detect recruitment of juveniles from the 2015 cohort to the lake. Given the dysconnectivity between Willow Creek and Clear Lake during the 2015 spawning season, the continued recruitment of young fish of this cohort to the lake may be attributed to reproduction by resident suckers in Willow Creek. Suckers younger than age-3 in Clear Lake could be identified as either shortnose or Klamath largescale suckers. A stream resident life history, if it were occurring, is consistent with these fish being Klamath largescale suckers. Survival of all distinguishable taxa of juvenile suckers is much higher in Clear Lake than in Upper Klamath Lake, with non-trivial numbers of suckers surviving to join spawning aggregations.

      Purpose and benefits of U.S. Geological Survey Trusted Digital Repositories

      Released June 11, 2020 09:25 EST

      2020, Fact Sheet 2020-3032

      Natalie Latysh, Keith G. Kirk, John Faundeen

      Federal mandates and U.S. Geological Survey (USGS, also known as the Bureau) Fundamental Science Practices (FSP) policies require that publicly funded scientific data, publications, and derivative works be openly accessible to researchers and the public. Open access helps to leverage the public investment by making the acquired data and published information products—collectively referred to as “data assets”—easier to locate, reproduce, and reuse. Open access also provides transparency to the processes used to acquire and analyze the data, thereby helping to ensure the scientific integrity of USGS data and products.

      The data assets produced by USGS programs, science centers, and projects are preserved digitally in various USGS and non-USGS repositories. To capitalize on the investment expended for data collection, analysis, and interpretation, these systems must remain useful and meaningful. For USGS repositories, the Bureau FSP Advisory Committee has implemented an evaluation process to ensure that the systems being used to preserve these data assets are trustworthy, reliable, and secure and thus provide for data longevity, integrity, and security. A system that is found to meet the reliability and suitability requirements is certified as a USGS Trusted Digital Repository.

      Groundwater levels and generalized potentiometric surfaces, former Naval Air Warfare Center, West Trenton, New Jersey, 2018

      Released June 09, 2020 12:00 EST

      2020, Open-File Report 2020-1016

      Alex R. Fiore, Pierre J. Lacombe

      Groundwater-level conditions, generalized groundwater potentiometric surfaces, and generalized flow directions at the decommissioned Naval Air Warfare Center in West Trenton, New Jersey, were evaluated for calendar year 2018. Groundwater levels measured continuously in five on-site wells and one nearby off-site well were plotted as hydrographs for January 1, 2018, through December 31, 2018. Groundwater levels measured in 110 wells on June 18, 2018, were contoured as generalized potentiometric surfaces on maps and sections. Generalized groundwater-flow directions inferred from the June 2018 data are shown in the maps and sections.

      Groundwater levels in six monitoring wells fluctuated in response to seasonal changes, precipitation, and pumping from “pump-and-treat” (P&T) wells. Record high precipitation totals in November, combined with a shutdown of three P&T wells in November, resulted in annual high water levels in late November for five of the six wells monitored. Annual high groundwater levels that occur during the fall are uncharacteristic of the typical timing of annual high water levels, which usually occur in the spring following low evapotranspiration during the winter months, compared to annual low water levels, which usually occur in fall because of high evapotranspiration during the summer months. The annual high water levels occurred following a 3-day precipitation event totaling 3.50 inches from November 24-26, which also caused the largest 1-day water-level increase for five of the six wells in 2018.

      The groundwater-level contour maps and sections include generalized flow directions. Given the heterogeneity of the site’s fractured rock aquifers, contours and associated groundwater-flow directions shown on the maps and sections should be considered as broad conceptualizations. A nearly vertical fault striking southwest to northeast separates the northwestern part of the site underlain by the Lockatong Formation from the southeastern part, which is underlain by the Stockton Formation. In the Lockatong Formation, general groundwater-flow directions were toward P&T wells. The P&T wells limited the flow of groundwater in the Lockatong Formation from the site into the adjacent areas and contained most groundwater contamination within the site. A groundwater divide bisected the site; groundwater in the western part generally flowed to P&T wells 8BR, 15BR, 20BR, 29BR, 56BR, 91BR, and BRP-2, and groundwater in the eastern part generally flowed to P&T well 48BR. A groundwater divide also was present in the Stockton Formation. Groundwater west of the divide in the Stockton Formation generally flowed toward P&T well 22BR, and groundwater east of the divide generally flowed south and southeast, away from the site. Saprolite and fill from land surface to depths of 25 feet below land surface exhibit similar properties to those of porous media, and water levels in surficial wells were contoured using a porous media aquifer approach. Water levels in these surficial wells indicate that groundwater in the saprolite and fill flowed predominantly toward Gold Run and, to a lesser extent, the West Ditch spring that drains to Gold Run. In addition, some shallow groundwater was captured by the cone of depression in the fractured bedrock and was attributed to P&T well 48BR.

      Acris blanchardi (Blanchard's Cricket Frog), Predation

      Released June 09, 2020 11:16 EST

      2020, Article

      Brittany R. Maldonado, Brad Glorioso, Raymond P. Kidder II

      Invertebrates are well-known predators of amphibians with many documented cases of spiders preying upon anurans (reviewed in Toledo 2005. Herpetol. Rev. 36:395–400). Wolf spiders are known to feed on a variety of frogs, including those in the genus Acris (Blackburn et al. 2002. Herpetol. Rev. 33:299). Although typically terrestrial, wolf spiders have been found feeding on arboreal frogs ca. 1 m above the ground (Aucone and Card 2002. Herpetol. Rev. 33:48). To our knowledge, no records exist of a wolf spider feeding on a terrestrial frog at an elevated height. At 0113 h on 30 April 2019, we observed an adult female wolf spider (Tigrosa georgicola: Lycosidae) feeding on an adult Acris blanchardi ca. 1.5 m high on the trunk of a small tree at the edge of a pond in Sherburne Wildlife Management Area, St. Martin Parish, Louisiana, USA (30.424°N, 91.663°W; WGS 84; Fig. 1). The spider was positioned facing the ground and the partially digested frog was hanging from its mouthparts. The spider likely captured the frog on the ground near the edge of the water and retreated up the tree with its meal (Fig. 1B). Movement of spiders with prey from an initial point of capture is documented in wolf spiders (Aucone and Card 2002, op. cit.) and other large terrestrial spiders (Maffei et al. 2010. Herpetol. Notes 3:167–170). This behavior may minimize the vulnerability of the spider to predators. We thank Zack Lemann, Curator of Animal Collections at the Audubon Butterfly Garden and Insectarium, for spider identification.

      Low-level detection of SFD-causing Ophidiomyces on Burmese Pythons in southwest Florida, with confirmation of the pathogen on co-occurring native snakes

      Released June 09, 2020 11:09 EST

      2020, Article

      Brad Glorioso, Ian A. Bartoszek, Jeffrey M. Lorch

      Snake fungal disease (SFD), or ophidiomycosis, is caused by the fungus Ophidiomyces ophiodiicola (Allender et al. 2015; Lorch et al. 2015). SFD is widespread across wild populations in the eastern United States (Lorch et al. 2016) and is known to infect more than 30 species of snake in North America and Europe (Lorch et al. 2016; Franklinos et al. 2017). No known phylogenetic or ecological patterns have been observed in susceptibility among snake taxa, and it is presumed that all species are likely susceptible (Burbrink et al. 2017).

      Observations on the structure of Surtsey

      Released June 09, 2020 07:44 EST

      2020, Surtsey Research (14) 33-45

      James G. Moore, Marie D. Jackson

      Comparison of investigations of the 1979 and 2017 cored boreholes coupled with continued observations of the dynamic surface of Surtsey has modified our concepts of the subsurface structure of the volcano. A geometrical analysis of the 2017 vertical and inclined cores indicates that near-surface layering dips westerly, indicating that the boreholes are located inside the Surtur crater. In subaerial deposits, as well as in deep deposits below sea level and below the pre-Surtsey seafloor, there are zones of porous tuff that contain abundant pyroclasts with narrow rims of fine ash. These features, typical of near-surface deposits, could have been carried down the vent by downslumping during fluctuating explosive activity. They support the hypothesis that a broad diatreme underlies the Surtur vent. No major intrusions were encountered in the 2017 drilling except for coherent basalt in deep sub-seafloor deposits below the center of Surtur crater. The 2017 borehole temperature measurements indicate that the peak temperature in the vertical boreholes was 124 °C at 105 meters below the surface (m.b.s.) and that in the inclined hole it was 127 °C at 115 m.b.s. immediately after drilling. These peak temperatures are 72 meters apart horizontally yet closely resemble each other in shape and magnitude, suggesting a broad heat source. In addition, measurements in the inclined hole from 200 to 290 m.b.s. indicate a temperature of 60±2 °C. This is apparently residual heat from the volcanic action that created the diatreme. These facts cast doubt on the previous concept that the heat anomaly in the 1979 borehole was due to a nearby intrusion. Instead they suggest that heat would have been conducted down from the 85-meter-thick hot lava shield within the Surtur crater into a warm diatreme substrate containing original volcanic heat. As the conducted heat moved down into the water-saturated substrate it would have elevated the temperature above the boiling point curve, baked out water, and created a vapor-dominated system below sea level. Eventually loss of heat by boiling and rise of steam caused the vapor-dominated system to retreat upward. The resulting steam rose and warmed the tephra adjacent to the lava shields where it produced broad areas of palagonitized tuff.

      Use of whole blood samples preserved in DNA lysis buffer for serological detection of avian malaria in Hawaiian forest birds

      Released June 08, 2020 08:39 EST

      2020, Report

      Carter T. Atkinson

      Recent detections of avian malarial parasites in native and non-native forest birds at Hakalau Forest National Wildlife Refuge and reports of epidemic transmission of the disease in high elevation habitats as well as controversy over accuracy of the PCR (polymerase chain reaction) diagnostic test that was being used led to a request by U.S. Fish and Wildlife Service to see if existing blood samples that were preserved in a DNA lysis buffer could be used for independent confirmation of the findings with antibody based serological methods. The primary objective of this study was to test whether some DNA buffers used for preservation of blood samples cause denaturation and loss of antigenicity of antibody molecules. If the buffer does not destroy antigenicity of these molecules, then the samples can be used in serological assays to provide an independent assessment of the accuracy of PCR tests.

      Source model for Sabancaya volcano constrained by DInSAR and GNSS surface deformation observation

      Released June 08, 2020 07:19 EST

      2020, Remote Sensing (12)

      Gregorio Boixart, Luis Cruz, Rafael Miranda, Pablo Euillades, Leonardo Euillades, Maurizio Battaglia

      Sabancaya is the most active volcano of the Ampato-Sabancaya Volcanic Complex (ASVC) in southern Perú and has been erupting since 2016. The analysis of ascending and descending Sentinel-1 orbits (DInSAR) and Global Navigation Satellite System (GNSS) datasets from 2014 to 2019 imaged a radially symmetric inflating area, uplifting at a rate of 35 to 50 mm/yr and centered 5 km north of Sabancaya. The DInSAR and GNSS data were modeled independently. We inverted the DInSAR data to infer the location, depth, and volume change of the deformation source. Then, we verified the DInSAR deformation model against the results from the inversion of the GNSS data. Our modelling results suggest that the imaged inflation pattern can be explained by a source 12 to 15 km deep, with a volume change rate between 26 × 106 m3/yr and 46 × 106 m3/yr, located between the Sabancaya and Hualca Hualca volcano. The observed regional inflation pattern, concentration of earthquake epicenters north of the ASVC, and inferred location of the deformation source indicate that the current eruptive activity at Sabancaya is fed by a deep regional reservoir through a lateral magmatic plumbing system.

      Fish and habitat assessment in Rock Creek, Klickitat County, southeastern Washington, 2018

      Released June 08, 2020 07:16 EST

      2020, Open-File Report 2020-1051

      Jill M. Hardiman

      Executive Summary

      Native steelhead (anadromous form of rainbow trout [Oncorhynchus mykiss]) and bridgelip sucker (Catostomus columbianus) were historically used by the Kah-miltpah (Rock Creek) Band for sustenance, trade, and traditional practices in Rock Creek, a tributary to the Columbia River in southeastern Washington State. Rock Creek flows south to the Columbia River at river kilometer (rkm) 368 and is an intermittent stream of great significance to the Yakama Nation and to the Kah-miltpah Band in particular. Concern over declines in the abundance of these fish in Rock Creek prompted a research and monitoring program to better understand habitat conditions, population status, and limiting factors. In addition to steelhead and bridgelip sucker, coho salmon (Oncorhynchus kisutch) and resident rainbow trout are also present and monitored. Rainbow trout and steelhead will be collectively referred to as O. mykiss. Streamflow is a limiting habitat factor in this system, but steelhead and coho salmon still successfully return to spawn, rear, outmigrate, and survive over summer in many of the isolated pools that provide important refuge for juvenile rearing.
      We completed a habitat survey during autumn 2018 to assess the perennial pools during low-flow conditions. In Rock Creek, the overall percentage of habitat recorded as dry was 41, non-pool wet was 42, and pool was 17. The number of pools (n=93) recorded was less than during previous years’ survey efforts (2015–17). The percentage of non-pool wet habitat was generally higher in 2018 than in previous years. This is a likely result of habitat reaches, which in the past, were considered pools but have become shallower and smaller and are now categorized as non-pool wet habitat. However, the fewer habitat reaches categorized as pools in 2018 now have an average length, area, and depth that are generally greater than in past years. In Walaluuks Creek, the percentage of habitat recorded as dry was 53, non-pool wet was 40, and pool was 7. The percentage of pool habitat was the lowest of all years surveyed since 2015.
      Fish sampling occurred during autumn after habitat surveys were completed from October 1 to November 9. Fish species distribution, relative abundance, length-frequency distribution, and pool fish density were determined using backpack electrofishing in stratified, systematically selected pools. During fish sampling, 855 O. mykiss were handled and 662 were tagged with a passive integrated transponder (PIT) tag, and 718 coho salmon were handled and 567 were PIT tagged. A total of 536 bridgelip suckers and largescale suckers (Catostomus macrocheilus [n=6]) were handled and 294 were PIT tagged. In Rock Creek, pool abundance estimates were calculated for six pools for both O. mykiss age classes (age 0 and age 1 or older [age 1+]) and one additional pool for age 1+. For pools where age-0 O. mykiss were present, the average pool population abundance was 0.144 (n=6; range: 0.052–0.208) fish per square meter. For age-1+ O. mykiss, the average pool population abundance was 0.045 (n=7; range: 0.002–0.179) fish per square meter. For age-0 O. mykiss in Walaluuks Creek, the average pool abundance was 0.207 fish per square meter (n=7; range: 0.038–0.416), and for age-1+ fish, the average pool abundance was 0.382 fish per square meter (n=6; range: 0.009–0.761). In Rock Creek, coho salmon were more abundant than O. mykiss in pools except for three pools upstream from rkm 20. The average pool abundance for coho salmon was 0.256 fish per square meter (n=8; range: 0.019–0.756) in Rock Creek pools. In Walaluuks Creek, coho salmon were captured in four pools and were not captured in the upstream pools sampled. The average pool abundance for coho salmon in the four lower pools was 0.488 fish per square meter (n=4; range: 0.417–0.548). Bridgelip suckers were captured in all pools in Rock Creek except the pool sampled at rkm 21.8. The average pool abundance for bridgelip suckers was 0.552 fish per square meter (n=7; range: 0.015–1.554) in Rock Creek. Bridgelip suckers were captured in three downstream pools in Walaluuks Creek, and the average abundance was 0.044 fish per square meter (n=3; range: 0.024–0.085).
      Overwinter and reach survival probabilities were estimated for O. mykiss and coho salmon using a Cormack-Jolly-Seber modeling approach. The best fit survival model for the O. mykiss and coho salmon was a reach only model. The upstream reach includes overwinter survival probability because fish are tagged and released in autumn and primarily migrate the following spring. During 2018, coho salmon (0.568, standard error [SE]=0.027) had a significantly higher probability of overwinter survival than O. mykiss (0.276, SE=0.019). The reach survival probability was higher for O. mykiss than coho salmon in the downstream migratory reaches. Survival was not modeled for bridgelip suckers. For bridgelip suckers, 147 were detected of 294, that were PIT tagged and released in the Rock Creek subbasin (50.0 percent).
      Information provided in this report increases our understanding of the status and trends of these populations. It further documents how intermittent streams can support salmonid populations. It also provides insight into potential management and restoration actions that could be beneficial and timing and allocation of resources. Ongoing monitoring work of this population will inform progress towards Rock Creek species recovery goals and contribution to recovery goals for the steelhead Middle Columbia River Distinct Population Segment.

      Incorporating spatial synchrony in the status assessment of a threatened species with multivariate analysis

      Released June 07, 2020 08:14 EST

      2020, Biological Conservation (248)

      Edward Stowe, Seth J. Wengerd, Mary C. Freeman, Byron J. Freeman

      Spatial synchrony—correlated abundance fluctuations among distinct populations—is associated with increased extinction risk but is not a component of widely-used extinction risk assessments (e.g., IUCN Red List, U.S. Fish and Wildlife Service’s Species Status Assessment). Alongside traditional viability metrics (i.e., the number of populations, their spatial extent, the status of each population), consideration of spatial synchrony in these assessments may provide additional insight into extinction risk as well as the relative importance of intrinsic and extrinsic factors on population dynamics. We demonstrate a method for estimating abundance trends in populations of the endangered freshwater fish, the amber darter (Percina antesella), while simultaneously assessing support for spatial synchrony among its two populations in the Conasauga and Etowah rivers in Georgia, U.S.A. Our analysis was performed using multivariate autoregressive state-space (MARSS) models with annual sampling data from 1996-2018 at 16 sites distributed between the two populations. Our results indicate that amber darter populations have declined substantially, with 9% annual losses in both the Conasauga and Etowah rivers, suggesting rangewide imperilment. Furthermore, model selection indicated little support for models with independent dynamics between rivers, which may compound overall extinction risk. This analysis demonstrates the utility of tools such as MARSS models for assessing spatial synchrony and long-term population trajectories of imperiled species, resulting in improved vulnerability assessments that do not assume independence among separate populations.

      Rock strength properties of granitic rocks in Yosemite Valley, Yosemite National Park, California

      Released June 05, 2020 10:02 EST

      2020, Data Series 1126

      Brian D. Collins, Federica Sandrone, Laurent Gastaldo, Greg M. Stock, Michel Jaboyedoff

      Yosemite National Park, located in the central part of California’s Sierra Nevada mountains, is a glacially carved landscape filled with iconic rock formations such as Cathedral Peak, El Capitan, and Half Dome. Igneous rocks, consisting primarily of variations of granite, granodiorite, and tonalite, make up the majority of the bedrock geology and their overall strength supports the spectacular cliffs and domes of Yosemite Valley that draw many visitors to the park. These same sheer cliffs also are the source areas for frequent rock falls, which, in addition to being the primary mechanism for cliff formation, can also pose a hazard to visitors and infrastructure located below.  To obtain rock strength parameters for use in assessing rock-fall potential in Yosemite National Park, we conducted a comprehensive rock mechanics laboratory testing program on a set of granitic rocks that form many of the cliffs in Yosemite Valley.

      Streambed scour of salmon (Oncorhynchus spp.) and steelhead (Oncorhynchus mykiss) redds in the South Fork Tolt River, King County, Washington

      Released June 04, 2020 13:38 EST

      2020, Scientific Investigations Report 2020-5044

      Andrew S. Gendaszek, Elizabeth Ablow, Derek Marks

      Prior to emergence as fry, salmonid embryos incubating within gravel nests called “redds” are vulnerable to substrate mobilization and lowering of the streambed, a process termed “streambed scour,” during floods. Water managers regulating discharge in salmonid-bearing rivers need information about the magnitude of discharge during which the scour of substrate surrounding salmonid redds occurs. The time when scour occurs, however, is difficult to measure and usually poorly constrained. The South Fork Tolt River in western Washington supplies the City of Seattle with hydroelectric power and about 40 percent of its municipal water needs, while providing spawning habitat for two salmonid species listed under the Endangered Species Act: Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (O. mykiss). The U.S. Geological Survey, in cooperation with Seattle City Light and Seattle Public Utilities, began a study in 2015 using accelerometer scour monitors (ASM) to characterize the timing of and hydrologic conditions associated with streambed scour at the depth of incubating salmonid embryos in the South Fork Tolt River. Prior to this study, operational thresholds for peak discharge on the South Fork Tolt River were 350 cubic feet per second (cfs) in the upper part of the river and 550 cfs in the lower part of the river as measured at USGS streamgages 12148000 and 12148300, respectively. These thresholds were developed from the peak discharge associated with observations of the flattening of redd structure and not from direct measurement of scour at the depth of egg pockets within redds. Accelerometer scour monitors were deployed at the level of salmonid egg pockets in spawning habitat of the South Fork Tolt River to record the temporal pattern of streambed scour at the depth of incubating salmon eggs during fall and winter flood seasons of water years (WY) 2016 and 2017. Thirteen of 48 ASMs deployed during the WY 2016 flood season recorded scour attributed to high streamflow when discharge measured at USGS streamgage 12148300 (the lower river streamgage used as an index gage) was between 969 and 1,360 cfs. Local discharge at individual scour sites varied depending on the timing of tributary inputs and downstream transport of water. During the subsequent flood season in WY 2017, peak discharge at the index gage reached 809 cfs. None of the 38 ASMs deployed recorded scour attributed to streamflow alone, although 10 ASMs recorded localized bed movement attributed to spawning activity of fish. Most scour at the depth of redds measured during WY 2016 occurred at or before peak flood discharge consistent with previous redd scour studies. The lack of scour measured in WY 2017 when peak discharge (809 cfs) was less than the minimum discharge when scour occurred in WY 2016 (969 cfs) suggests minimal to no scour of egg pockets in salmonid redds when discharge is less than 809 cfs.

      Subspecies differentiation in an enigmatic chaparral shrub species

      Released June 04, 2020 11:05 EST

      2020, American Journal of Botany

      Yi Huang, Glen R. Morrison, Alan Brelsford, Janet Franklin, Diana D Jolles, Jon Keeley, V Thomas Parker, Natalie Saavedra, Andrew C Sanders, Thomas Stoughton, Gregory A. Wahlert, Amy Litt


      Delimiting biodiversity units is difficult in organisms in which differentiation is obscured by hybridization, plasticity, and other factors that blur phenotypic boundaries. Such work is more complicated when the focal units are subspecies, the definition of which has not been broadly explored in the era of modern genetic methods. Eastwood manzanita (Arctostaphylos glandulosa Eastw.) is a widely distributed and morphologically complex chaparral shrub species with much subspecific variation, which has proven challenging to categorize. Currently 10 subspecies are recognized, however, many of them are not geographically segregated, and morphological intermediates are common. Subspecies delimitation is of particular importance in this species because two of the subspecies are rare. The goal of this study was to apply an evolutionary definition of “subspecies” to characterize structure within Eastwood manzanita.


      We used publicly available geospatial environmental data and reduced‐representation genome sequencing to characterize environmental and genetic differentiation among subspecies. In addition, we tested whether subspecies could be differentiated by environmentally associated genetic variation.


      Our analyses do not show genetic differentiation among subspecies of Eastwood manzanita, with the exception of one of the two rare subspecies. In addition, our environmental analyses did not show ecological differentiation, though limitations of the analysis prevent strong conclusions.


      Genetic structure within Eastwood manzanita does not correspond to current subspecies circumscriptions, but rather reflects geographic distribution. Our study suggests that subspecies concepts need to be reconsidered in long‐lived plant species, especially in the age of next‐generation sequencing.

      Safe work practices for working with wildlife

      Released June 03, 2020 15:06 EST

      2020, Techniques and Methods 15-C2

      Tegwin Taylor, Danielle Buttke

      Katherine L. D. Richgels, Samantha E.J. Gibbs, Margaret A. Wild, editor(s)

      Most wildlife biologists, technicians, and veterinarians complete their tasks safely and uneventfully every day. However, some significant risks exist in this line of work, and injuries, illnesses, and accidental deaths among wildlife workers do occur. Aviation accidents (airplane and helicopter), drownings, and car and truck accidents are the most common causes of fatalities among wildlife workers (Sasse, 2003). Although rare, serious zoonotic infections also happen. Being mindful of occupational hazards and zoonoses (diseases transmitted between humans and animals), and the various ways to minimize these risks, can help workers stay safe and healthy on the job.

      Optimization of tidal marsh management at the Cape May and Supawna Meadows National Wildlife Refuges, New Jersey, through use of structured decision making

      Released June 03, 2020 11:35 EST

      2020, Open-File Report 2020-1055

      Hilary A. Neckles, James E. Lyons, Jessica L. Nagel, Susan C. Adamowicz, Toni Mikula, Brian Braudis, Heidi Hanlon

      Structured decision making is a systematic, transparent process for improving the quality of complex decisions by identifying measurable management objectives and feasible management actions; predicting the potential consequences of management actions relative to the stated objectives; and selecting a course of action that maximizes the total benefit achieved and balances tradeoffs among objectives. The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, applied an existing, regional framework for structured decision making to develop a prototype tool for optimizing tidal marsh management decisions at the Cape May and Supawna Meadows National Wildlife Refuges in New Jersey. Refuge biologists, refuge managers, and research scientists identified multiple potential management actions to improve the ecological integrity of 13 marsh management units within the refuges and estimated the outcomes of each action in terms of performance metrics associated with each management objective. Value functions previously developed at the regional level were used to transform metric scores to a common utility scale, and utilities were summed to produce a single score representing the total management benefit that would be accrued from each potential management action. Constrained optimization was used to identify the set of management actions, one per marsh management unit, that would maximize total management benefits at different cost constraints at the refuge scale. Results indicated that, for the objectives and actions considered here, total management benefits may increase consistently up to approximately $785,000, but that further expenditures may yield diminishing return on investment. Management actions in optimal portfolios at total costs less than $785,000 included applying sediment to the marsh surface (thin layer deposition) in seven marsh management units, controlling the invasive reed Phragmites australis in four marsh management units, remediating hydrologic alterations in two marsh management units, and planting native vegetation in one marsh management unit. The management benefits were derived from expected improvements in the capacity for marsh elevation to keep pace with sea-level rise, increases in numbers of spiders (as an indicator of trophic health) and tidal marsh obligate birds, and increased cover of native vegetation. The prototype presented here provides a framework for decision making at the Cape May and Supawna Meadows National Wildlife Refuges that can be updated as new data and information become available. Insights from this process may also be useful to inform future habitat management planning at the refuges.