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Publications recently added to the Pubs Warehouse

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Simulation of Water Availability in the Southeastern United States for Historical and Potential Future Climate and Land-Cover Conditions

Released June 19, 2019 15:45 EST

2019, Scientific Investigations Report 2019-5039

Jacob H. LaFontaine, Rheannon M. Hart, Lauren E. Hay, William H. Farmer, Andy R. Bock, Roland J. Viger, Steven L. Markstrom, R. Steven Regan, Jessica M. Driscoll

A study was conducted by the U.S. Geological Survey (USGS), in cooperation with the Gulf Coastal Plains and Ozarks Landscape Conservation Cooperative (GCPO LCC) and the Department of the Interior Southeast Climate Adaptation Science Center, to evaluate the hydrologic response of a daily time step hydrologic model to historical observations and projections of potential climate and land-cover change for the period 1952–2099. The model simulations were used to compute the potential changes in hydrologic response and streamflow statistics across the Southeastern United States, using historical observations of climate and streamflow. Thirteen downscaled general circulation models with four representative concentration pathways were used to represent a range of potential future changes in climate (a total of 45 future simulations) from the Coupled Model Intercomparison Project Phase 5. The streamflow statistics were selected to describe streamflow conditions that may be most useful in defining the suitability for each river or stream to support sustaining populations of priority aquatic species across the GCPO LCC. An application of the Precipitation-Runoff Modeling System (included as part of the USGS National Hydrologic Model) was used to develop the hydrologic simulations. The results showed increases in air temperature across the study area, with the highest increases occurring in the northern part of the study area during July to September. The results showed a mix of increases and decreases in precipitation accumulation across the study area and across seasons, with decreases in precipitation accumulation across all seasons for the southwestern part of the study area. Actual evapotranspiration decreased for the southeastern part of the study area and increased for the northwestern part of the study area. The results showed general decreases in runoff across the study area, with increases in runoff in areas surrounding large metropolitan regions where potential future increases in impervious area occur. Results from a statistical analysis (Kolmogorov-Smirnov test) showed that the downscaled general circulation models generally have more skill in producing historical streamflow statistics in the duration and magnitude categories and less skill in producing historical streamflow statistics in the frequency, rate of change, and timing categories for this study area. The potential changes in the streamflow statistics and the results of the Kolmogorov-Smirnov test are available through the GCPO LCC Conservation Planning Atlas, an online science-based mapping platform built specifically for land managers and planners.

Development of a Flood-Inundation Map Library and Precipitation-Runoff modeling for the Clear Fork Mohican River in and near Bellville, Ohio

Released June 19, 2019 15:15 EST

2019, Scientific Investigations Report 2019-5017

Chad J. Ostheimer, Carrie A. Huitger

The U.S. Geological Survey (USGS), in cooperation with the Muskingum Watershed Conservancy District, led hydrologic and hydraulic analyses within the Clear Fork Mohican River Basin in and near Bellville, Ohio. The analyses included the development of digital flood-inundation maps for an approximately 2.5-mile reach of the Clear Fork Mohican River and the development of a precipitation-runoff model for a portion of the Clear Fork Mohican River Basin.

Data collection for the study involved the installation and operation of 2 streamgages (Clear Fork Mohican River at Bellville, Ohio, and Cedar Fork above Bellville, Ohio); 1 lake-level gage (Clear Fork Reservoir near Lexington, Ohio); 2 precipitation gages (Clear Fork Reservoir near Lexington, Ohio, and Rain Gage at Cedar Fork above Bellville, Ohio); and 12 submersible pressure transducers on Clear Fork Mohican River and 4 of its tributaries. Data collection also included field surveys of hydraulic structures and channel cross sections.

Flood profiles were computed for the 2.5-mile reach of the Clear Fork Mohican River by means of a one-dimensional step-backwater model. The model was calibrated to 16 measured events and to a portion (stages 9 to 11 feet) of the current stage-streamflow relation at the USGS streamgage Clear Fork Mohican River at Bellville, Ohio, and to stage recorded at a submersible pressure transducer site near the downstream study limit. After calibration the step-backwater model was used to compute nine flood profiles for stages ranging from 9 to 17 feet. The flood profiles were then used in combination with a digital elevation model to delineate the area that would be inundated at each stage.

A precipitation-runoff model was developed and calibrated using data from the streamgage, precipitation gage, and 11 submersible pressure transducers. The modeling included data during 10 runoff events that were used for model calibration and validation, with focus on 6 events. The Nash-Sutcliffe model efficiency coefficients for six peak streamflow events ranged from 0.459 to 0.851.

The models produced by this study can be used to assess possible flood mitigation options and define flood hazard areas that could contribute to the protection of life and property. The availability of flood-inundation maps, internet information from USGS streamgages, and forecasted stages from the National Weather Service could provide emergency management personnel and residents with information on forecasting floods, appropriate flood response activities, and post-flood recovery efforts.

Arsenic in Chinese coals: Distribution, modes of occurrence, and environmental effects

Released June 18, 2019 18:25 EST

2011, Article

Y. Kang, Guijian Liu

Arsenic, one of the most hazardous elements occurring in coals, can be released to the environment during coal processing and combustion. Based on the available literature and published results obtained in our laboratory, the content, distribution and the modes of occurrence of As in Chinese coals, and its environmental and impacts are reviewed in this article. With the 4763 sets of data (from the literature) rearranged, the arithmetic mean As concentration of each province and weighted mean As concentration of the entire country (using the expected coal reserves as the weighting factor) were calculated. The weighted mean As concentration in Chinese coals is 3.18 mg/kg, with As concentration increasing from northern China to southern China. The As concentration in coal varies with coal-forming ages and coal ranks. Arsenic has several modes of occurrence in coals. According to results obtained by other studies and our own experiments, As is mainly associated with mineral matter (such as pyrite and other sulfide minerals) in coals, although a significant amount of arsenic is associated with organic matter. The accumulation of As in coal is controlled by many geological factors during coal-forming processes, including plant decomposition, sedimentary environments, and epigenetic hydrothermal activity. During the combustion of coal, As is released to the air, water, and soil, causing serious environmental pollution. More than 45% of the coal consumed in China is utilized by power plants, and it is estimated that nearly 522 tonnes, 21 tonnes and 252 tonnes of As are emitted into the atmosphere by industries, residential buildings and coal-fired power plants, respectively, every year.

Monitoring protocol development and assessment for narrowly endemic toads in Nevada, 2018

Released June 18, 2019 15:33 EST

2019, Open-File Report 2019-1067

Brian J. Halstead, Patrick M. Kleeman, Adam Duarte, Jonathan P. Rose, Kris Urquhart, Chad Mellison, Kevin Guadalupe, Melanie Cota, Rachel Van Horne, Alexa Killion, Kelsey Ruehling

Several species and subspecies of toads are endemic to small spring systems in the Great Basin, and their restricted ranges and habitat extent make them vulnerable to environmental perturbations. Very little is known about several of these toad populations, so a group of stakeholders including the U.S. Geological Survey, U.S. Fish and Wildlife Service, Bureau of Land Management, Nevada Department of Wildlife, the U.S. Navy, U.S. Forest Service, and Oregon State University met to discuss information needs on these populations and to develop a monitoring protocol that would detect population changes over time. In cooperation with the U.S. Fish and Wildlife Service, the U.S. Geological Survey implemented the proposed survey protocol, a multi-state occupancy design, for three sites: Dixie Valley, Railroad Valley, and Hot Creek, to evaluate its ease of implementation and effectiveness. We found that the multi-state occupancy protocol worked well in the Dixie Valley and, with some refinement, would likely work well in the Railroad Valley. We suggest that capture-mark-recapture of adults might be a more effective approach at Hot Creek. For most life stages of most populations, detection probabilities were positively related to survey duration up to 20 minutes, and the best time of day to conduct surveys varied by life stage and population. We make population-specific suggestions for the number of surveys and their timing and duration. Annual surveys using the suggested survey protocols will likely allow estimation of trends in the proportion of area of each population existing in different population states (occupied, occupied with evidence of reproduction, and unoccupied) and in most cases can be readily implemented with minimal training or handling of toads.

iCoast – Did the Coast Change?: Storm-impact model verification using citizen scientists

Released June 18, 2019 15:20 EST

2019, Conference Paper, Proceedings of the 9th International Conference Coastal Sediments 2019

Karen L M Morgan, Nathaniel G. Plant, Hilary F. Stockdon, Richard J. Snell

The USGS provides model predictions of severe storm impacts prior to landfall based on pre-storm morphology and predicted total water levels, including waves and surge. Presented in near real time on the USGS Coastal Change Hazard Portal, they provide coastal residents, scientists, and emergency managers valuable coastal response information. iCoast – Did the Coast Change?, an online tool for comparing pre- and post-storm photography, allows volunteer citizen scientist help researchers classify storm impacts through aerial photography. Using spatially matched pre- and post-storm image pairs from Hurricane Sandy, iCoast users identified the coastal processes seen in each image. These classifications were compared to the predictive model probabilities just prior to Sandy’s landfall. User classifications agreed with the model predictions with a high degree of confidence for dune erosion and overwash. However, for inundation, user classifications, limited to observations of island breaching, were less confident and should be used with caution

Summary of climatic, geographic, geologic, and available hydrologic data and identification of data gaps for the Black Bear Creek watershed of the Pawnee Nation Tribal Jurisdictional Area, Oklahoma

Released June 18, 2019 10:34 EST

2019, Scientific Investigations Report 2019-5043

Matthew S. Varonka

The Pawnee Nation is compiling a comprehensive water-management plan for the Pawnee Nation Tribal Jurisdictional Area in north-central Oklahoma. One of the first steps needed in preparing such a plan is a summary and analysis of available hydrologic data and reports that have been published for the area. In phase I of a three-phase, watershed-based approach to summary and analysis of water resources of the Pawnee Nation, the U.S. Geological Survey, in cooperation with the Pawnee Nation and Bureau of Indian Affairs, conducted a literature search and data analysis for the Black Bear Creek watershed within the Pawnee Nation Tribal Jurisdictional Area, referred to herein as the “Black Bear Creek study area.” This report summarizes the available data for the Black Bear Creek study area.

Climatic, geographic, geologic, water-use, and hydrologic data from previously published reports or databases were collected and analyzed for this report. Because of the limited amount of groundwater-quality data for the study area, a field collection of groundwater levels and water samples was conducted. Sixteen wells were identified, and groundwater levels were measured at each well. Eight wells were sampled, and water properties, major ions, and nutrients were measured.

Overall, there are few long-term monitoring stations to help determine trends of surface-water quality, groundwater quality, and groundwater levels across the study area. Establishing and maintaining long-term streamflow, surface-water-quality, groundwater-level, and groundwater-quality monitoring sites would greatly increase the understanding of the water resources in the Black Bear Creek study area. Additionally, water-use estimates would be greatly improved by metering groundwater withdrawals. Establishing hydrologic and water-quality trends and having improved estimates of water use can aid decision makers in the stewardship of the water resources in this area.

This report can aid the Pawnee Nation in prioritization of future projects and serve as a background document for the development of a jurisdiction-wide comprehensive water-management plan.

2019 Joint Agency Commercial Imagery Evaluation—Land remote sensing satellite compendium

Released June 17, 2019 15:27 EST

2019, Circular 1455

Jon B. Christopherson, Shankar N. Ramaseri Chandra, Joel Q. Quanbeck

The Joint Agency Commercial Imagery Evaluation (JACIE) is a collaboration between five Federal agencies that are major users and producers of satellite land remote sensing data. In recent years, the JACIE group has observed ever-increasing numbers of remote sensing satellites being launched. This rapidly growing wave of new systems creates a need for a single reference for land remote sensing satellites that provides basic system specifications and linkage to any JACIE assessment that may have been completed on existing systems. This volume has been assembled by the Requirements, Capabilities, and Analysis for Earth Observation Project under the U.S. Geological Survey National Land Imaging Program as a contribution to the JACIE community. This is the first edition of the JACIE compendium, which is planned to be updated and released annually.

Monitoring storm tide from Hurricane Michael along the northwest coast of Florida, October 2018

Released June 17, 2019 14:42 EST

2019, Open-File Report 2019-1059

Michael J. Byrne Sr.

Hurricane Michael made landfall near Mexico Beach and Tyndall Air Force Base in the Florida Panhandle, with maximum sustained winds over 160 miles per hour, on October 10, 2018. The maximum recorded storm tide was 15.55 feet above the North American Vertical Datum of 1988 (NAVD 88). The elevation of the maximum high-water mark, found in Port St. Joe, Florida, exceeded 20 feet above NAVD 88. The storm tide and winds destroyed much of the tourist town of Mexico Beach and caused extensive damage to the surrounding communities, including Tyndall Air Force Base, Panama City Beach, Port St. Joe, and Cape San Blas, Fla.

The U.S. Geological Survey (USGS), in cooperation with Federal Emergency Management Agency and Florida Division of Emergency Management, deployed a temporary monitoring network of water-level and barometric pressure sensors at 34 sites along the northwest coast of Florida to record the timing, areal extent, and magnitude of hurricane storm tide generated by Hurricane Michael. A total of 522 high-water marks were recovered and surveyed from 331 sites from Seaside, Fla. to Cedar Key, Fla. The USGS, in cooperation with Federal Emergency Management Agency and Florida Division of Emergency Management, displays real-time water-level data from long-term USGS streamflow stations, rapid deployment gages and National Oceanic and Atmospheric Administration tide-gage stations, updated hourly (or, in some cases, more frequently), through satellite telemetry, on the USGS Flood Event Viewer (https://stn.wim.usgs.gov/FEV/#Michael2018).

Great Lakes Cladophora harbors phylogenetically diverse nitrogen-fixing microorganims

Released June 17, 2019 14:38 EST

2019, Environmental DNA

Muruleedhara Byappanahalli, Meredith Nevers, Katarzyna Przybyla-Kelly, Satoshi Ishii, Timothy L. King, Aaron Aunins

Abstract Nitrogen‐fixing microorganisms are among the epiphytic communities in Cladophora, potentially benefitting the algae in nutrient‐deficient waters, but their abundance and diversity remain unexplored. In this study, we determined the abundance and taxonomic composition of these nitrogen‐fixing microorganisms in Cladophora growing on rocks, breakwall structures, or submerged dreissenid mussel beds around southern Lake Michigan (N = 33) during the summer 2015, using two complementary genomic techniques: quantitative PCR (qPCR) and shotgun metagenomic sequencing. Genomic DNA was extracted from processed algal pellets, and the nitrogen‐fixing microbes were quantified by qPCR by targeting the nifH gene. Mean nifH concentrations (log10 copy numbers/gram algae fresh weight ± SE) were 5.54 ± 0.09, ranging from 4.31 to 6.57. Mean nifH concentrations in water samples (log10 copy numbers/milliliter of water ± SE) were: 3.25 ± 0.06, ranging from 2.41 to 3.90. Shotgun sequencing of a subset of algal samples representing the four sampling locations (N = 10) revealed as many as 267 nifH reads from among the sequences of the 10 shotgun metagenomes (averaging 27 reads per metagenome), ranging from 5 to 91 reads from Jeorse Park (September) and North Beach (September) locations. Taxonomic assignment of nifH sequences identified members from bacteria and archaea domains showing a clear separation of reads at domain and lower taxonomic levels. Bacteria were relatively more abundant than archaea. Anabaena, Bradyrhizobium, Geobacter, Methylocystis, Oscillatoria sp., and Skermanella (all bacteria), and Methanoregula, Methanothrix, and Methanosarcina (archaea) were among the nitrogen‐fixing genera identified by the MEGAN Community Edition program. Collectively, these findings show that phylogenetically diverse nitrogen‐fixing microbial communities are part of the Cladophora microbiome, likely contributing to the algal nitrogen needs.

Evaluation of streambed-sediment metals concentrations in the Spring River Basin, Cherokee County Superfund site, Kansas, 2017

Released June 17, 2019 10:42 EST

2019, Scientific Investigations Report 2019-5046

Brian J. Klager, Kyle E. Juracek

To evaluate the magnitude of, and change in, mining-related contamination, streambed-sediment samples were collected from 30 sampling sites in the Spring River Basin in the Cherokee County Superfund site, southeast Kansas, in July and August 2017. The Cherokee County Superfund site is part of the Tri-State Mining District, an area that covers parts of Kansas, Missouri, and Oklahoma that was historically mined for lead and zinc. The sampling sites corresponded to 30 sites sampled in 2004 as part of a previous study.

Concentrations of cadmium, lead, and zinc in the 2017 streambed-sediment samples were compared with the 2004 concentrations and with available sediment-quality guidelines. Cadmium concentrations from 2004 and 2017 samples were not compared if both samples had concentrations less than the lower of the sediment-quality guidelines because of poor performance of cadmium replicate-samples analyses at lower concentrations. Streambed-sediment concentrations of cadmium, lead, and zinc in the 2017 samples compared to the 2004 samples were decreased by at least 20 percent at 12, 16, and 16 sites, respectively; increased by at least 20 percent at 2, 5, and 7 sites, respectively; and had less than a 20-percent change at 5, 9, and 7 sites, respectively. In 2017, cadmium, lead, and zinc concentrations exceeded general consensus-based sediment-quality guidelines at 17, 14, and 18 sites, respectively, compared to 19, 17, and 20 sites, respectively, in 2004. In 2017, cadmium, lead, and zinc concentrations exceeded Tri-State Mining District-specific sediment-quality guidelines at 12, 14, and 11 sites, respectively, compared to 16, 16, and 13 sites, respectively, in 2004. The highest 2017 concentrations of cadmium, lead, and zinc were measured at sites along Short Creek near Galena, Kansas.

Statistics of petroleum exploration in the world outside the United States and Canada through 2015

Released June 17, 2019 09:45 EST

2019, Circular 1450

Emil D. Attanasi, Philip A. Freeman

The world’s future oil and gas supplies depend on existing reserves and the additions to those reserves that may result, in part, from ongoing exploration and new discoveries. This Circular summarizes available oil and gas exploration data for the world outside the United States and Canada (the study area) through 2015. It updates U.S. Geological Survey Circulars 981, 1096, and 1288 (by D.H. Root, E.D. Attanasi, and R.L. Turner, 1987; E.D. Attanasi and D.H. Root, 1993; and E.D. Attanasi, P.A. Freeman, and J.A. Glovier, 2007). The exploration measures focus on the search for undiscovered conventional oil and gas accumulations.

The goal of this compilation, presentation, and analysis of exploration and discovery data is to identify, at the reconnaissance level, the areas explored for oil and gas and to characterize their degree of exploration maturity. Maps and graphs provide a visual summary of the exploration maturity of an area. The maps include both land and offshore areas. The maps show delineated prospective areas, which are the industry-defined areas of interest in the search for undiscovered conventional oil and gas accumulations. The maps also show explored areas, which are areas where the density of exploration and development drilling rules out new discoveries of large conventional petroleum accumulations.

Whereas the maps show the static state of oil and gas exploration, the dynamic measures of exploration progress are characterized graphically. The graphs show the growth in the delineated prospective and explored areas as a function of wildcat drilling. The relation between the expansion of the delineated prospective area and the rate of wildcat drilling is determined by the siting of the wildcat wells. Additional graphs show the magnitude of discoveries tied to specific delineated prospective areas. These graphs provide a way to evaluate the quality, in terms of discovered oil and gas, of areas identified by the dates when each area became prospective.

From 2006 through 2015, the delineated prospective area within the study area expanded at a rate of about 48,100 square miles per year. This is slightly above the expansion rate of 46,200 square miles per year from 1996 through 2005. From 2006 through 2015, the explored area expanded at a rate of about 12,900 square miles per year, which is somewhat greater than the rate of 11,300 square miles per year for the period from 1996 through 2005. The delineated prospective area established by 1970 accounts for 35 percent of the delineated prospective area established through 2015 but contains 70 percent of the oil and 52 percent of the natural gas discovered through 2015. From 2006 through 2015, offshore discoveries accounted for 71 percent of the oil and 78 percent of the gas discovered in the study area and 40 percent of the offshore wildcat wells were drilled in deep offshore areas (deeper than 200 meters water depth).

The delineated prospective area and explored area calculated with oil and gas wells and fields at depths of at least 10,000 feet are less than half of the respective areas calculated with all oil and gas wells and fields. The discovery histories of most regions indicate that average discovery sizes are generally larger in deeper geologic horizons. To correctly interpret the exploration maturity of a deep horizon, drilling and discovery data must be considered in the context of the geology of the area. Such analyses should be prepared at the level of the petroleum basin or subbasin.

Technical comment on “Global pattern of nest predation is disrupted by climate change in shorebirds”

Released June 14, 2019 11:26 EST

2019, Science

Martin Bulla, Jeroen Reneerkens, Emily L. Weiser, Aleksandr Sokolov, Audrey R. Taylor, Benoit Sittler, Brian J McCaffery, Daniel R. Ruthrauff, Daniel H. Catlin, David C. Payer, David H. Ward, Diana V Solovyeva, Eduardo SA Santos, Eldar Rakhimberdiev, Erica Nol, Eunbi Kwon, Glen S Brown, Glenda D Hevia, H. River Gates, James A. Johnson, Jan A. van Gils, Jannik Hansen, Jean-Francois Lamarre, Jennie Rausch, Jesse R. Conklin, Joe Liebezeit, Joel Bety, Johannes Lang, Jose A Alves, Juan Fernandez-Elipe, Klaus-Michael Exo, Loic Bollache, Marcelo Bertellotti, Marie-Andree Giroux, Martijn van de Pol, Matthew D. Johnson, Megan L. Boldenow, Mihai Valcu, Mikhail Soloviev, Natalya Sokolova, Nathan R. Senner, Nicholas Lecomte, Nicolas Meyer, Niels Martin Schmidt, Olivier Gilg, Paul A Smith, Paula Machin, Rebecca L McGuire, Ricardo AS Cerboncini, Richard Ottvall, Rob SA van Bemmelen, Rose J Swift, Sara T Saalfeld, Sara E Jamieson, Stephen C. Brown, Theunis Piersma, Tomas Albrecht, Veronica L D'Amico, Richard B. Lanctot, Bart Kempenaers

Kubelka et al. (Report, 9 November 2018, p. 680-683) claim that climate change has disrupted patterns of nest predation in shorebirds. They report that predation rates have increased since the 1950s, especially in the Arctic. We describe methodological problems with their analyses and argue that there is no solid statistical support for their claims.

Methods for installation, removal, and downloading data from the temperature profiling probe (TROD)

Released June 14, 2019 10:43 EST

2019, Open-File Report 2019-1066

Ramon C. Naranjo

This document provides a brief method overview on the deployment and removal of the temperature profiling probe developed by the U.S. Geological Survey (USGS) in 2015 and referred to as SensorRod or temperature rod (TROD). The TROD is suitable for short- to long-term deployments (days to years) for evaluating thermal gradients in soils and sediments beneath surface water. Applications include evaluating exchange between groundwater and surface water, seepage losses in agricultural canals, infiltration on hillslopes, and timing of snowmelt and runoff. The temperature sensors inside the TROD are iButtons and are meant to be replaceable when needed. The housing is water tight and is made of schedule 80 PVC pipe. Sensor intervals are flexible and can be built to specific applications.

A joint patent (U.S 10/180,360.) and license agreement between the USGS and Alpha Mach for the TROD design was obtained in 2019, and a paper in Water Resource Research describes the design and testing (Naranjo and Turcotte, 2015).

Hydrologic and hydraulic analyses of selected streams in Richland County, Ohio

Released June 13, 2019 15:11 EST

2019, Scientific Investigations Report 2019-5011

Chad J. Ostheimer

Hydrologic and hydraulic analyses were done for selected reaches of Clear Fork Mohican River and Cedar Fork in Richland County, Ohio. To update and expand a portion of the Federal Emergency Management Agency detailed Flood Insurance Study, the U.S. Geological Survey (USGS) and the Muskingum Watershed Conservancy District initiated a cooperative study. The study comprised an 18.6-mile reach of the Clear Fork Mohican River and a 5.9-mile reach of Cedar Fork.

Historical streamflow data from the streamgage Clear Fork Mohican River at Bellville, Ohio (USGS station number 03131982) and regional regression equations were used to estimate instantaneous peak streamflows for floods with 10-, 4-, 2-, 1-, and 0.2-percent and 1-percent plus annual exceedance probabilities. The 1-percent plus flood elevation is defined by the Federal Emergency Management Agency as a flood elevation derived by using streamflows that include the average predictive error for the regression equation streamflow calculation for the Flood Risk project. This error is then added to the 1-percent annual exceedance probability flood streamflow to calculate the new 1-percent plus streamflow.

The annual exceedance probability streamflows were then used in a Hydrologic Engineering Center-River Analysis System step-backwater model to determine water-surface elevation profiles and flood-inundation boundaries for the 10-, 4-, 2-, 1-, and 0.2-percent and 1-percent plus annual exceedance probability floods and a regulatory floodway along a selected reach of each stream. The Clear Fork Mohican River model was calibrated to 16 flood events by using the current stage-streamflow relation at the streamgage Clear Fork Mohican River at Bellville, Ohio (USGS station number 03131982) and a submersible pressure transducer. Flood-inundation boundaries for the 1- and 0.2-percent annual exceedance probability floods and a regulatory floodway were mapped for each stream.

Water resources of Tensas Parish, Louisiana

Released June 13, 2019 14:21 EST

2019, Fact Sheet 2019-3004

Vincent E. White

Information concerning the availability, use, and quality of water in Tensas Parish, Louisiana, is critical for proper water-supply management. The purpose of this fact sheet is to present information that can be used by water managers, parish residents, and others for stewardship of this vital resource. In 2014, 38.01 million gallons per day (Mgal/d) of water were withdrawn in Tensas Parish, including about 33.02 Mgal/d from groundwater sources and about 4.99 Mgal/d from surface-water sources. Withdrawals for agricultural use, composed of general irrigation, rice irrigation, aquaculture, and livestock, accounted for about 97 percent (36.88 Mgal/d) of the total water withdrawn. Other use categories included public supply and rural domestic. Water-use data collected at 5-year intervals from 1960 to 2010 and again in 2014 indicated that water withdrawals peaked in 2014. The large increase in 1985 relative to 1980 and 1990 for groundwater usage is likely an outlier that is attributable to a change in methodology for estimating rice irrigation. A transition in available farm-by-farm data from 1980 to 1985 to 1990 resulted in three different methods being used for estimating groundwater withdrawals for rice irrigation.

Benthic foraminiferal biotic events related to the Paleocene–Eocene Thermal Maximum along the California Margin

Released June 13, 2019 13:05 EST

2019, Marine Micropaleontology (150)

Kristin McDougall-Reid, Cedric M John

The faunal expression of the Paleocene-Eocene Thermal Maximum (PETM) is well documented in deep-sea sediments. However, few studies have examined continental margin sections, especially active margins. The Moreno and Lodo formations, Central California, were deposited along the eastern margin of a north-south trending forearc basin on the convergent margin of California during the Cretaceous through Late Cenozoic. The Tumey Gulch section which includes the Moreno and Lodo formations, is 80 m thick, contains the Paleocene-Eocene boundary and Carbon Isotope Excursion (CIE), and was deposited at abyssal to lower bathyal depths along an active continental margin. Benthic foraminiferal assemblages from this section record faunal changes related to the PETM and a younger hyperthermal, ETM3 which include a disruption of the gradual shallowing of water depths and fluctuation of the CCD. Associated with the onset of the hyperthermals in this section is a red clay-siltstone layer (low calcium carbonate content) and an increase in smoothly finished dissolution resistant agglutinated benthic foraminiferal species which corresponds with a rapid shoaling of the CCD. The subsequent overcompensation is identified by a rapid change to shallower benthic biofacies faunas, increased sediment rate, current activity, and terrestrial organic matter which is associated with increased weathering. Further analysis of the foraminiferal faunas identified the benthic foraminiferal extinction event (BEE), deep water agglutinated faunal acmes, and fluctuations in the calcareous foraminiferal assemblages which indicate changes in the paleoenvironmental conditions (e.g. dissolved oxygen, sedimentation rates and current activity, and the influx of organic carbon) during the PETM and ETM3. The Ynezian, Bulitian, and Penutian California benthic foraminiferal stages are recognized in the Tumey Gulch section as well as the benthic foraminiferal extinction event (BEE) which occurs at the onset of the PETM and is distinguished by the last appearance of Paleocene species and the first appearance of many Eocene species. Agglutinated foraminiferal species dominate the late Paleocene through early Eocene part of the section indicating deposition occurred at abyssal depths below the CCD and that the environment was oligotrophic with moderate to low organic flux. The Glomospira acme zone is recognized at the base of the CIE and just above the top of red clay-siltstone layer and suggests increased terrestrial organic matter and elevated sedimentation rates. The abundance of calcareous species, specifically Bulimina alazanensis, followed by the appearance of opportunistic taxa (Tappanina and Quadrimorphina) in the PETM interval indicates deposition within the lower bathyal biofacies and a drop in the depth of the CCD. Eocene species characteristic of the Survivor faunal group (Anomalinoides, Bulimina, Cibicidoides, and Pleurostomella) appear above this event. Foraminiferal assemblages dominated by agglutinated foraminifera appear in sediments overlying the PETM interval and indicate deposition occurred at abyssal depths and below the CCD. Calcareous foraminiferal assemblages appear higher in the section as water depths decrease. The presence of a second red clay-siltstone layer associated with a second isotope excursion and faunal changes in the upper part of the section indicate the presence of another hyperthermal, ETM3.

Assessment of the presence of sewage in the Mill River under low-flow conditions, Springfield, Massachusetts, 2010–11

Released June 13, 2019 09:15 EST

2019, Scientific Investigations Report 2019-5027

Andrew J. Massey, Marcus C. Waldron, R. Jean Tang, Thomas G. Huntington

The U.S. Geological Survey, in cooperation with the Pioneer Valley Planning Commission, the U.S. Environmental Protection Agency, and the Massachusetts Department of Environmental Protection Senator William X. Wall Experiment Station, assessed the presence of 14 commonly used human-health pharmaceutical compounds, fecal indicator bacteria, and other man-made compounds indicative of the presence of human sewage in the lower reach of the Mill River near its confluence with the Connecticut River in Springfield, Massachusetts. The study was part of the Tri-State Connecticut River Targeted Watershed Initiative and involved the collection and analysis of raw river water at three sites along the reach, extending from Watershops Pond to the mouth, over the course of a low-flow period, July through November 2010. Previous studies in the region indicated that nonpoint or undocumented sources of wastewater contributed a variety of organic contaminants and potentially harmful bacteria to rivers under both high- and low-flow conditions. Additional samples, including a raw sewage sample collected near a Mill River combined sewer overflow during a non-overflow period, were collected in March 2011.

The study was designed to determine if city sewage or other domestic sources of wastewater were entering the river within this reach during low-flow conditions. No definitive evidence of sewage was measured in Mill River water samples collected during the study period. Fecal indicator bacteria, including Escherichia coli (E. coli) and enterococci bacteria, were detected in all Mill River water samples. In the DNA analysis of enterococci cultures from the Mill River, samples generally tested negative for the Enterococcus faecium (esp) human-specific genetic marker, whereas the raw sewage sample tested positive. Samples also generally tested negative in the human-specific rDNA marker assay for the anaerobic bacterium Bacteroidetes. Samples tested negative in 2010 for two Bacteroidetes human-specific genetic markers, HF134 and HF183, except samples from near the mouth of the Mill River, which tested positive. Samples collected in March 2011 from all three measurement sites tested positive for both markers. The results of bacterial analyses suggest that the fecal bacteria in summer and fall months are most likely of animal origin rather than human. Despite the urban setting, long history of development, and many potential sources of man-made contamination in the Mill River, none of the 12 water samples collected during the study contained targeted pharmaceutical compounds at concentrations greater than the analytical reporting levels. Other man-made compounds, like fluorescent whitening agents, were measured and detected in samples at low concentrations 4 out of 5 times the samples were collected; however, the other lines of evidence do not support a sewer source but rather other nonpoint sources upstream in the watershed.

The results of this study do not support the hypothesis that aging sewer lines or combined sewer overflow infrastructure leak into the Mill River as tested during the low-flow conditions during sampling for this study. None of the results from Mill River samples offer conclusive evidence of the presence of sewage. Some low-level detections of pharmaceutical compounds, other man-made chemicals, and bacteria suggest an upstream, nonpoint source.

A single raw sewage sample was collected, diluted, and examined for comparison with Mill River water samples and to ensure that the analytical methods could detect typical wastewater constituents. High levels of bacteria were measured, and low levels of three anthropogenic pharmaceutical compounds were detected, confirming the effectiveness of the sub-part-per-million method. The concentration of fluorescent whitening agent-1 in the sewage sample was 90,000 times greater than the median concentration in the Mill River samples.

Soil characteristics are associated with gradients of big sagebrush canopy structure after disturbance

Released June 11, 2019 14:21 EST

2019, Ecosphere (10)

David Barnard, Matthew J. Germino, Robert Arkle, John Bradford, Michael Duniway, David Pilliod, David Pyke, Robert Shriver, Justin Welty

Reestablishing shrub canopy cover after disturbance in semi-arid ecosystems, such as sagebrush steppe, is essential to provide wildlife habitat and restore ecosystem functioning. While several studies have explored the effects of landscape and climate factors on the success or failure of sagebrush seeding, the influence of soil properties on gradients of shrub canopy structure in successfully seeded areas remains largely unexplored. In this study, we evaluated associations between soil properties and gradients in sagebrush canopy structure in stands that had successfully reestablished after fire and subsequent seeding treatments. Using a dataset collected across the Great Basin, USA, of sagebrush stands that had burned and reestablished between 1986 and 2013, we tested soil depth and texture, soil surface classification, biological soil crusts plus mean historical precipitation, solar heatload, and fire history as modeling variables to explore gradients in sagebrush canopy structure growth in terms of cover, height, and density. Deeper soils were associated with greater sagebrush canopy structure development in terms of plant density and percent cover, coarser textured soils were associated with greater sagebrush cover and density, and more clayey soils were typically associated with greater height. Biological crust presence was also positively associated with enhanced sagebrush canopy growth, but adding more demographically or morphologically explicit descriptions of biocrust communities did not improve explanatory power. Increasing heatload had a negative effect on sagebrush canopy structure growth, and increased mean annual precipitation was only associated with greater sagebrush height. Given that conservation and restoration of the sagebrush steppe ecosystems has become a priority for land managers, the associations we identify between gradients in post-fire sagebrush canopy structure growth and field-identifiable soil characteristics may improve planning of land treatments for sagebrush restoration and the understanding of semi-arid ecosystem functioning and post-disturbance dynamics.

Interpretation of dye tracing data collected November 13–December 2, 2017, at the Savoy Experimental Watershed as part of the Advanced Groundwater Field Techniques in Karst Terrains course, Savoy, Arkansas

Released June 11, 2019 14:00 EST

2019, Scientific Investigations Report 2019-5016

Eve L. Kuniansky, Joshua M. Blackstock, Daniel M. Wagner, J. Van Brahana

The first course on the use of advanced groundwater field techniques for karst aquifers was conducted November 13–17, 2017, at the University of Arkansas Savoy Experimental Watershed (SEW), which is located on pastures for beef livestock research conducted by the Department of Animal Sciences at the University of Arkansas at Savoy, Arkansas. The SEW is an interdisciplinary, collaborative, long-term research site for the study of animal-waste management in a mantled karst setting. The course focused on advanced field activities appropriate for karst aquifer studies: dye tracing, groundwater/surface-water interactions, geophysical methods, and geochemistry. This report summarizes the data collected and interpreted from the dye tracing part of the November 2017 course, other USGS field courses, and past dye tracing investigations conducted by University of Arkansas students.

Changes in hydrodynamics and wave energy as a result of seagrass decline along the shoreline of a microtidal back-barrier estuary

Released June 11, 2019 13:59 EST

2019, Advances in Water Resources (128) 183-192

Carmine Donatelli, Neil Kamal Ganju, Tarandeep S. Kalra, S Fagherazzi, Nicoletta Leonardi

Seagrasses are marine flowering plants that provide key ecological services. In recent decades, multiple stressors have caused a worldwide decline in seagrass beds. Changes in bottom friction associated with seagrass loss are expected to influence the ability of estuarine systems to trap sediment inputs through local and regional changes in hydrodynamics. Herein, we conduct a numerical study using six historical maps of seagrass distribution in Barnegat Bay, USA, to demonstrate that reductions in seagrass coverage destabilize estuarine systems, decreasing their flood-dominance in the areas interested by seagrass disappearance and increasing bed-shear stress values across the entire back-barrier basin. Furthermore, we reveal how seagrass decline has considerably increased the impact of wind-waves on marsh edges between 1968 and 2009. From a comparison with a numerical experiment without submerged aquatic vegetation, we estimate that up to 40% of the computed wave thrust on marsh boundaries can be reduced by seagrass beds and we find that the location of a seagrass patch in addition to its aerial extent plays a crucial role in this attenuation process. This study highlights the benefits of seagrass meadows in enhancing estuarine resilience and reducing marsh-edge retreat by wind-wave attack, which is recognized as a chief agent in lateral marsh loss.

The roles of flow acceleration and deceleration in sediment suspension in the surf zone

Released June 11, 2019 12:30 EST

2019, Conference Paper, Coastal Sediments 2019, Proceedings of the 9th International Conference

Bruce E. Jaffe, Seanpaul La Selle

Prediction of sediment suspension in the surf zone remains elusive. We explore how suspended sediment concentration at 19 cm above the bed in the mid-surf zone during a storm is influenced by flow acceleration and deceleration. There is a tendency for higher suspended sediment concentrations during onshore flow, with decelerating onshore flows having higher concentrations than steady, accelerating, or reversing flows. The development of models that exploit information on flow acceleration, deceleration, and flow reversal may lead to improved ability to predict suspended sediment transport in the surf zone and resulting geomorphic changes.

Evaluating the sustainability of a Cisco Fishery in Thunder Bay, Ontario under alternate harvest control rules

Released June 11, 2019 10:06 EST

2019, North American Journal of Fisheries Management

Nicholas C Fisch, James R. Bence, Jared T. Myers, Eric K. Berglund, Daniel Yule

Sustainable management of fish stocks is promoted through the application of Management Strategy Evaluations, providing information to managers on the relative performance of alternative management approaches (strategies) while accounting for uncertainty. In this study, we developed a simplified management strategy evaluation of a cisco, Coregonus artedi, stock in Thunder Bay, Ontario, to determine both the sustainability of the current harvest control rule (i.e., a constant exploitation rate of 10%) and the performance of alternative harvest control rules in meeting fishery objectives. Our simulations explicitly accounted for uncertainty in the frequency of strong year classes being produced by cisco, the stock-recruit relationship, stock abundance, and the sex-specific nature of roe harvest. Assuming future productivity is similar to that observed over the past 30 years, results suggest the current exploitation rate of 10% is sustainable in terms of maintaining spawning biomass above 20% of the unfished level. Variants of constant exploitation rate control rules that included biomass thresholds defining when exploitation rate is to decrease as a function of spawning stock size increased yield, decreased risk, and increased the magnitude of spawning biomass at the end of the simulation period. However, these advantages came at the expense of greater inter-annual variation in yield. Constant catch control rules greatly underperformed constant exploitation rate control rules in terms of magnitude in yield. Constant catch control rules, however, did reduce inter-annual variation in yield compared to constant exploitation rate control rules. Furthermore, conditional versions of constant catch control rules (i.e., threshold stock sizes below which catch limit was reduced) mitigated risks of staying at low stock size.

Is barotrauma an important factor in the discard mortality of Yellow Perch?

Released June 11, 2019 09:58 EST

2019, Journal of Fish and Wildlife Management (10) 69-78

Carey Knight, Richard T. Kraus, Demetra Panos, Ann Marie Gorman, Benjamin Leonhardt, Jason Robinson, Michael J. Thomas

In physoclistous fishes, barotrauma caused by rapid decompression during capture may be an important source of fishing mortality that is unquantified for some fisheries. We developed a predictive logistic model for barotrauma incidence in Yellow Perch Perca flavescens and applied this model to Ohio's recreational and commercial fisheries in Lake Erie where fisheries managers implicitly consider discard mortality to be negligible in current stock assessment. As expected, capture depth explained most of the variation in incidence, with comparatively small effects of season, sex, and size categories. Measurements of whole body and gonad density provided limited explanation for the categorical effects. Both fisheries spanned a range of depths (7.6 to 16.8 m) that corresponded to a broad range of barotrauma incidence (13 to 74%). Using a recent example, we estimated that additional fishing mortality due to barotrauma in discards was approximately six-fold higher in the commercial than recreational fishery. Overall, this additional mortality was <1% of lake-wide population size estimates. Thus, the assumption that all discarded Yellow Perch survive is unlikely to result in a detectable bias in population estimates. One caveat is that we still do not understand how strong year-classes might influence discard mortality via increased discard rate and barotrauma incidence for small fish.

Aquatic vegetation and invertebrate communities of Big Stone National Wildlife Refuge

Released June 11, 2019 09:54 EST

2019, Journal of Fish and Wildlife Management (1) 277-294

Brian Tangen, Raymond Finocchiaro, Wesley E. Newton, Charles F. Dahl

Observed degradation of aquatic systems at Big Stone National Wildlife Refuge, located in west-central Minnesota, have been associated with sediment-laden inflows from riverine systems. To support management, a study was conducted during 2013–2014 with overall goals of characterizing the aquatic invertebrate and vegetation communities of the Big Stone National Wildlife Refuge and exploring relations between these communities and various water-quality parameters. Sample sites were located along an observed vegetation gradient and assigned to three predetermined habitat zones for comparison purposes: upstream, transition, and downstream. Of the 12 species of aquatic vegetation that were identified, invasive narrowleaf cattail Typha angustifolia dominated the upstream zone (observed at .90% of sample locations), coontail Ceratophyllum demersum and narrowleaf cattail were most common in the transition zone (collected or observed at 100 and 83% of sample locations, respectively), and coontail and narrowleaf pondweed Potamogeton strictifolius were most common in the downstream zone collected at 100 and 64% of sample locations, respectively). Measured values for the water-quality parameters varied among dates, reflecting the continually fluctuating nature of riverine systems. Based on general observations across sample dates, turbidity and dissolved oxygen concentrations were greatest in the upstream zone sample sites, while oxidation-reduction potential was greatest in the downstream zone sites. There were 115 unique aquatic invertebrate taxa identified to varying levels of taxonomic resolution. Results suggested that there were overall differences in invertebrate biomass among the sample dates, but that there were no strong trends among the sample zones. Aquatic invertebrates and vegetation communities, along with the water-quality parameters, varied temporally and showed irregular relations among the sample zones. These general observations emphasize the importance of temporally and spatially intensive sampling to account for natural variation. Moreover, short- and long-term streamflow and water-level information obtained for this study demonstrated substantial variability that must be considered when conducting biotic inventories and monitoring water quality, as well as when using such data to assess management options. Periodic monitoring of wetlands and associated streamflows, along with sediment loads and water quality of inflows, should allow Big Stone National Wildlife Refuge staff to identify habitat degradation and potential contributing factors, and to develop strategies to achieve specific management objectives and goals.

Assessment of continuous oil and gas resources in the Beetaloo Basin, Australia, 2018

Released June 10, 2019 16:45 EST

2019, Fact Sheet 2019-3013

Christopher J. Schenk, Tracey J. Mercier, Cheryl A. Woodall, Thomas M. Finn, Kristen R. Marra, Michael E. Brownfield, Heidi M. Leathers-Miller, Ronald M. Drake II

Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean resources of 429 million barrels of continuous oil and 8 trillion cubic feet of continuous gas in the Beetaloo Basin of northern Australia.

Regional hydraulic geometry characteristics of stream channels in the Ouachita Mountains of Arkansas

Released June 10, 2019 15:40 EST

2019, Data Series 1104

Aaron L. Pugh, Ronald K. Redman

Many stream channel infrastructure, habitat, and restoration projects are being undertaken on small streams throughout Arkansas by various Federal, State, and local agencies and by private organizations and businesses with limited data on local geomorphology and streamflow relations. Equations are needed that relate drainage area above stable stream reaches and the associated basin characteristics to bankfull streamflow and the associated channel dimensions. These equations, along with streambed material particle information, provide information that can improve stream channel projects. The U.S. Geological Survey and the Arkansas Natural Resources Commission in cooperation with the U.S. Army Corps of Engineers, Little Rock District, undertook a study to develop these equations for streams in the Ouachita Mountains of Arkansas.

Seventeen streamgages operated by the U.S. Geological Survey, located on streams in the Ouachita Mountains, were selected for analysis. Regional hydraulic geometry curves that express the mathematical relation between the bankfull channel dimensions (cross-sectional area, top width, mean depth, and streamflow) and the contributing drainage areas were developed. Streambed material measurements were collected to develop descriptive statistics of the streambed particle-size distributions and percentages of substrate type at each study site. Stream reaches at each study site were classified to the Rosgen level II stream type based on the average of stream channel metrics collected from site cross sections and profiles. Of the 17 selected Ouachita Mountain stream reaches, 6 were classified as B stream types, and 11 were classified as C stream types. The B stream types have infrequently spaced pools; very stable plan forms, profiles, and banks; and narrow, gently sloping valleys, where bank vegetation is a moderate component of stability. The C stream types are meandering, point bar, riffle-pool channels associated with broad valleys having well-defined flood plains and terraces composed of alluvial soils, where bank vegetation is typically a high component of stability.

Post-fire rockfall and debris-flow hazard zonation in the Eagle Creek Fire burn area, Columbia River Gorge, Oregon: a tool for emergency managers and first responders

Released June 10, 2019 15:05 EST

2019, Conference Paper, Association of Environmental and Engineering Geologists; special publication 28

Nancy C. Calhoun, William J. Burns, S.H. Hayduk, Dennis M. Staley, Jason W. Kean

The Eagle Creek Fire engulfed 48,832 acres (196 km2) within the Columbia River Gorge, Oregon beginning September 2nd and was 100% contained by November 30th, 2017. The Columbia River Gorge area is steep and heavily forested characterized by cliffs and flanking talus slopes, receiving > 100 inches (> 254 cm) of precipitation annually. The Columbia River Gorge is a critical lifeline for Oregon and Washington, including interstate highway 84 (I-84) and state route 14 (SR-14), commercial train lines, freight traffic, major pipelines, shipping corridor, 1,000s of permanent residents, tourists and motorists, and major hydroelectric dams. Before the Eagle Creek Fire, there was significant landslide and debris-flow hazard. More than 80 landslides have been recorded in the Gorge during the last ~100 years, with 58 of these recorded in the exceptionally wet and stormy winters of 1996 and 1997. Several of these landslides damaged property and temporarily closed I-84, train and ship traffic. There is some uncertainty on the degree to which the fire will enhance debris-flow susceptibility, because the climate, terrain and geology is different from the regions where most post-fire debris-flow research has been conducted. A large portion of the Columbia River Gorge National Scenic Area, including popular hiking trails, remain closed 18 months after the fire, with the Historic Columbia River Highway opened 14 months after the fire. In the aftermath of the Eagle Creek Fire, emergency managers and first responders identified a critical need for a post-fire landslide response plan and hazard map. The Oregon Department of Transportation (ODOT), the Oregon Department of Geology and Mineral Industries (DOGAMI), and the U.S. Geological Survey (USGS) participated in the creation of the plan including making a landslide hazard map specific to their outlook, which includes swift decision making during emergencies such as landslide or flood events. This paper presents a perspective of post-fire debris flow-hazard response and assessment from the Eagle Creek burn area in the Columbia River Gorge, Oregon.

Taking the pulse of debris flows: Extracting debris-flow dynamics from good vibrations in southern California and central Colorado

Released June 10, 2019 14:53 EST

2019, Conference Paper, Association of Environmental and Engineering Geologists, Special Publication #28

A. Michel, Jason W. Kean, Joel B. Smith, Kate E. Allstadt, Jeffrey A. Coe

The destructive nature of debris flows makes it difficult to quantify flow dynamics with direct instrumentation. For this reason, seismic sensors placed safely away from the flow path are often used to identify the timing and speed of debris flows. While seismic sensors have proven to be a valuable tool for event detection and early warning, their potential for identifying other aspects of debris flows (such as sediment concentration) is less studied. Here we use two monitoring sites to investigate the extent to which debris-flow dynamics can be decoded from ground vibrations. One site is a bedrock channel in a steep semiarid basin in central Colorado (Chalk Cliffs), and the other is in a debris-flow channel incised in alluvium in a recently burned area in southern California (Van Tassel). At both sites, seismic data are measured with geophones (4.5 Hz) mounted next to the channels and sampled at high frequencies (500-1000 Hz). Independent constraints on flow dynamics are provided by laser distance meters to record flow stage (at 10 Hz) and high-definition video cameras to record flow velocity and sediment concentration. The observed debris flows at Chalk Cliffs typically consist of a series of short-duration (~30 second) surges with total durations of <40 minutes and have coarse-grained fronts and fluid-rich tails. In contrast, the events at Van Tassel are longer duration flows (>40 minutes) that begin as debris flows and transform into more steady debris floods. The arrangement of sensors at both sites allow us to identify correlations between vertical ground velocity, frequency, flow stage, and qualitative estimates of sediment concentration.

Microbiomes of stony and soft deep-sea corals share rare core bacteria

Released June 10, 2019 11:17 EST

2019, Microbiome

Christina A. Kellogg

Background: Numerous studies have shown that bacteria form stable associations with host corals and have focused on identifying conserved “core microbiomes” of bacterial associates inferred to be serving key roles in the coral holobiont. Because studies tend to focus on only stony corals (order Scleractinia) or soft corals (order Alcyonacea), it is currently unknown if there are conserved bacteria that are shared by both. A meta-analysis was done of 16S rRNA amplicon data from multiple studies generated via identical methodology to allow direct comparisons of bacterial associates across seven deep-sea corals, including both stony and soft species: Anthothela grandiflora, Anthothela sp., Lateothela grandiflora, Lophelia pertusa, Paramuricea placomus, Primnoa pacifica, and Primnoa resedaeformis.

Results: Twenty-three operational taxonomic units (OTUs) were consistently present in greater than 50% of the coral samples. Seven amplicon sequence variants (ASVs), five of which corresponded to a conserved OTU, were consistently present in greater than 30% of the coral samples including five or greater coral species. A majority of the conserved sequences had close matches with previously identified coral-associated bacteria. While known to dominate tropical and temperate coral microbiomes, Endozoicomonas were extremely rare or absent from these deep-sea corals. An Endozoicomonas OTU associated with Lo. pertusa in this study was most similar to those from shallow-water stony corals, while an OTU associated with Anthothela spp. was most similar to those from shallow-water gorgonians.

Conclusions: Bacterial sequences have been identified that are conserved at the level of class Anthozoa (i.e., found in both stony and soft corals, shallow and deep). These bacterial associates are therefore hypothesized to play important symbiotic roles and are highlighted for targeted future study. These conserved bacterial associates include taxa with the potential for nitrogen and sulfur cycling, detoxification, and hydrocarbon degradation. There is also some overlap with kit contaminants that need to be resolved. Rarely detected Endozoicomonas sequences are partitioned by whether the host is a stony coral or a soft coral, and the finer clustering pattern reflects the hosts’ phylogeny.

Assessment of tight-oil and tight-gas resources in the Junggar and Santanghu Basins of Northwestern China, 2018

Released June 10, 2019 11:00 EST

2019, Fact Sheet 2019-3012

Christopher J. Potter, Christopher J. Schenk, Tracey J. Mercier, Marilyn E. Tennyson, Thomas M. Finn, Cheryl A. Woodall, Heidi M. Leathers-Miller, Kristen R. Marra, Phuong A. Le, Ronald M. Drake II, Michael E. Brownfield, Janet K. Pitman

Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean resources of 241 million barrels of tight oil and 10.1 trillion cubic feet of tight gas in the Junggar and Santanghu Basins of northwestern China.

Hydrogeologic characterization of part of the Lower Floridan aquifer at the South District Wastewater Treatment Plant, Miami-Dade County, Florida

Released June 10, 2019 07:19 EST

2019, Open-File Report 2019-1034

Kevin L. DeFosset, Kevin J. Cunningham

The South District Wastewater Treatment Plant in southeastern Miami-Dade County, Florida, includes a Class I treated wastewater injection well system. The detection of ammonia in monitoring zones above the injection zone in the Lower Floridan aquifer has elicited a need to understand the nature of confinement within the Lower Floridan aquifer as it pertains to the vertical migration of injectate out of the injection zone upward into the Underground Source of Drinking Water in the upper part of the Floridan aquifer system. Geologic and geophysical data, borehole video imagery, and aquifer performance data were used to refine and clarify the geologic and hydrogeologic frameworks of part of the Lower Floridan aquifer at the treatment plant. The data provide evidence for zones of enhanced dissolution permeability, extensive secondary porosity, fractures, karst collapse structures, and faults that could provide vertical cross-formational fluid pathways that transect the Lower Floridan aquifer.

Geographic variation in the intensity of warming and phenological mismatch between Arctic shorebirds and invertebrates

Released June 08, 2019 10:09 EST

2019, Ecological Monographs

Enubi Kwon, Emily L. Weiser, Richard B. Lanctot, Stephen C. Brown, H. River Gates, H. Grant Gilchrist, Steve J. Kendall, David B. Lank, Joseph R. Liebezeit, Laura McKinnon, Erica Nol, David C. Payer, Jennie Rausch, Sarah T. Saalfeld, Daniel J. Rinella, Nathan R. Senner, Paul A. Smith, David Ward, Robert C. Wissman, Brett K. Sandercock

Responses to climate change can vary across functional groups and trophic levels, leading to a temporal decoupling of trophic interactions or ‘phenological mismatches.’ Despite a growing number of single-species studies that identified phenological mismatches as a nearly universal consequence of climate change, we have a limited understanding of the spatial variation in the intensity of this phenomenon nor what influences this variation. In this study, we tested for geographic patterns in phenological mismatches between six species of shorebirds and their invertebrate prey at ten sites spread across ~13º latitude and ~84º longitude in the Arctic over three years. At each site, we quantified the phenological mismatch between shorebirds and their invertebrate prey at: 1) an individual nest level, as the difference in days between the seasonal peak in food and the peak demand by chicks, and 2) a population level, as the overlapped area under fitted curves for total daily biomass of invertebrates and dates of the peak demand by chicks. We tested whether the intensity of past climatic change observed at each site corresponded with the extent of phenological mismatch and used Structural Equation Modeling to test for causal relationships among: 1) environmental factors, including geographic location and current climatic conditions, 2) the timing of invertebrate emergence and the breeding phenology of shorebirds, and 3) the phenological mismatch between the two trophic levels. The extent of phenological mismatch varied more among different sites than among different species within each site. A greater extent of phenological mismatch at both the individual-nest and population-levels coincided with changes in the timing of snowmelt as well as the potential dissociation of long-term snow phenology from changes in temperature. The timing of snowmelt also affected the shape of the food and demand curves, which determined the extent of phenological mismatch at the population level. Finally, we found larger mismatches at more easterly longitudes, which may be affecting the population dynamics of shorebirds, as two of our study species show regional population declines in only the eastern part of their range. This suggests that phenological mismatches may be resulting in demographic consequences for arctic-nesting birds.

Inundation, flow dynamics, and damage in the 9 January 2018 Montecito Debris-Flow Event, California, USA: Opportunities and challenges for post-wildfire risk assessment

Released June 07, 2019 14:26 EST

2019, Geosphere

Jason W. Kean, Dennis M. Staley, Jeremy T. Lancaster, Francis K. Rengers, Brian J. Swanson, Jeffrey A. Coe, Janis . Hernandez, Aaron Sigman, Kate E. Allstadt, Donald N. Lindsay

Shortly before the beginning of the winter rainy season, one of the largest fires in California history (Thomas Fire) substantially increased the susceptibility of steep slopes in Santa Barbara and Ventura Counties to debris flows. On January 9, 2018, before the fire was fully contained, an intense burst of rain fell on the portion of the burn area above Montecito, CA. The rainfall and associated runoff triggered a series of debris flows that mobilized approximately 680,000 m3 of sediment (including boulders >4 m) at velocities up to 4 m/s down urbanized alluvial fans. The resulting destruction (including 23 fatalities, at least 167 injuries, and 408 damaged homes) underscores the need for improved understanding of debris-flow runout in the built environment, and the need for a comprehensive framework to assess the potential loss from debris flows following wildfire. We present observations of the inundation, debris-flow dynamics, and damage from the event. The data include field measurements of flow depth and deposit characteristics made 12 days after the event (before ephemeral features of the deposits were lost to recovery operations); an inventory of building damage; estimates of flow velocity; information on flow timing; soil-hydrologic properties; and post-event imagery and lidar. Together, these data provide rare spatial and dynamic constraints for testing debris-flow runout models, which are needed for advancing post-fire debris-flow hazard assessments. Our analysis also outlines a framework for translating the results of these models into estimates of economic loss based on an adaptation of the Federal Emergency Management Agency’s Hazus model for tsunamis.

Viable long-term gas hydrate testing site confirmed on the Alaska north slope

Released June 06, 2019 15:37 EST

2019, Fire in the Ice: NETL Methane Hydrate Newsletter (19) 1-5

Ray Boswell, Scott Marsteller, Nori Okinaka, Motoi Wakatsuki, Timothy S. Collett, Robert Hunter, Tom Walsh, David Itter, Stephen Crumley

In December 2018, data acquired in a Stratigraphic Test Well drilled from the 7-11-12 pad in the western part of the Prudhoe Bay Unit, Alaska North Slope confirmed the occurrence of two high-quality reservoirs fully saturated with gas hydrate. The drilling was the initial phase of a planned, three-well program designed to conduct an extended duration test of the response to gas hydrate reservoirs to controlled depressurization. The Stratigraphic Test Well (formally “PBU Hydrate-01”) was operated by the PBU Operator BP Exploration, (Alaska), Inc. (BPXA) using the Parker 272 drilling rig (Figure 1) through a Drilling Services Agreement executed with Petrotechnical Resources of Alaska (PRA) in association with a contract between NETL and PRA. The science program executed by BPXA was developed over a two-year period through extensive discussions and scientific evaluation undertaken by NETL, the Japan, Oil, Gas, and Metals, National Corporation (JOGMEC), the U.S. Geological Survey (USGS), and PRA. The effort also benefitted greatly from the support of the Alaska Department of Natural Resources (ADNR) and the PBU Working Interest Owners (WIOs). 

Statistical power of dynamic occupancy models to identify temporal change: Informing the North American Bat Monitoring Program

Released June 06, 2019 15:14 EST

2019, Ecological Indicators (105) 166-176

Katherine Banner, Kathryn M. Irvine, Tom J Rodhouse, Deahn M. Donner, Andrea R. Litt

Dynamic occupancy models provide a flexible framework for estimating and mapping species occupancy patterns over space and time for large-scale monitoring programs (e.g., the North American Bat Monitoring Program (NABat), the Amphibian Research and Monitoring Initiative). Challenges for designing surveys using the dynamic occupancy modeling framework include defining appropriate derived trend parameters, and providing usable tools for researchers to conduct project-specific sample size investigations. We present a simulation-based power analysis framework for dynamic occupancy models that allows for the incorporation of the underlying environmental space (i.e., as covariates) within a specific study region to inform sample size estimation. We investigate two definitions of temporal trend: (1) a gradual, sustained (linear or nonlinear) change over a period of many years, and (2) an abrupt increase or decrease between two time periods. We draw upon pilot data collected following NABat protocols to inform assumed data generating values in a demonstration of our approach. Due to the complicated parameter structure of dynamic occupancy models, we emphasize the importance of visualizing simulated changes over time based on different parameter settings prior to conducting a power analysis. Our simulations revealed that the linearity of short-term trends (five years in our investigation) conferred higher power with lower sample size than longer trends where occupancy probabilities approached zero (ten years in our investigation). We provide an example of how to use our tools to conduct customized investigations using questions posed by NABat, and in doing so, we shed light on general guidelines that can be applied to programs monitoring species occupancy for other taxa. Importantly, we created an R package to execute our approach for informing program-, species-, and study-specific investigations aimed at identifying changes in species occupancy.

Measuring settling velocity in a strongly tidal estuary

Released June 06, 2019 13:40 EST

2019, Conference Paper, Coastal Sediments 2019, Proceedings of the 9th International Conference

Rachel (Contractor) Allen, Jessica R. Lacy, Evan A Variano

Predicting sediment transport in estuarine systems requires understanding sediment settling velocity, its range of fluctuations, and the shortcomings of the tools to measure it. Previous studies have used Laser In-Situ Scattering and Transmissometry (LISST) instruments to measure particle size and Acoustic Doppler Velocimeters (ADV) to return estimates of settling velocity. We deployed both instruments over a 4-week period in summer 2016 in San Pablo Bay, CA, and observed conflicting results from the two instruments. The LISST indicated the settling velocity decreased with increasing bed shear stress, while the ADV showed that settling velocity increased. Comparing the experimental conditions from this study with previous research reveals that the ADV method requires steady state conditions that were not achieved. Although the ADV method uses easily measured quantities to return the settling velocity, it relies on assumptions that are not always valid in estuarine settings.

Biota dose assessment of small rodents sampled near breccia pipe uranium mines in the Grand Canyon watershed

Released June 06, 2019 10:16 EST

2019, Health Physics (117) 20-27

Kelsey M. Minter, Timothy Jannik, Jo Ellen Hinck, Danielle Cleveland, Walter P. Kubilius, Wendy W. Kuhne

The biotic exposure and uptake of radionuclides and potential health effects due to breccia pipe uranium mining in the Grand Canyon watershed are largely unknown. This paper describes the use of the RESRAD-BIOTA dose model to assess exposure of small rodents (n = 11) sampled at three uranium mine sites in different stages of ore production (active and postproduction). Rodent tissue and soil concentrations of naturally occurring uranium (234U, 235U, and 238U), thorium (228Th, 230Th, and 232Th), and radium (226Ra) radioisotopes were used in the dose model. The dose assessment results indicated that the potential internal, external, and total doses to rodents were below the US Department of Energy’s biota dose standard of 1 mGy d−1. As expected, tissue concentrations of 238U, 234U, and 230Th were in approximate equilibrium; however, 226Ra results in tissue were 1.25 to 5.75 times greater than 238U, 234U, and 230Th tissue results for 10 out of 11 samples. Soil at the three sites also displayed 226Ra enrichment, so it is likely that the 226Ra enrichment in the rodents was from soil via typical activities (i.e., burrowing, incidental ingestion, bathing, etc.) or by dietary uptake of translocated 226Ra. The results suggest that 226Ra is more mobile in this environment and bioaccumulates in these rodent species (e.g., in bones via the bloodstream). Internal dose accounting suggests that 226Ra is the radionuclide of most concern for rodent exposure and health.

Water Resources of West Carroll Parish, Louisiana

Released June 06, 2019 07:59 EST

2019, Fact Sheet 2018-3069

Vincent E. White

Information concerning the availability, use, and quality of water in West Carroll Parish, Louisiana, is critical for proper water-supply management. The purpose of this fact sheet is to present information that can be used by water managers, parish residents, and others for stewardship of this vital resource. In 2014, 21.27 million gallons per day (Mgal/d) of water were withdrawn in West Carroll Parish, including 17.91 Mgal/d from groundwater sources and 3.37 Mgal/d from surface-water sources. Withdrawals for agricultural use, composed of general irrigation, rice irrigation, and livestock, accounted for 93 percent (19.76 Mgal/d) of the total water withdrawn. Other use categories included public supply and rural domestic. Water-use data collected at 5-year intervals from 1960 to 2010 and again in 2014 indicated that water withdrawals peaked in 2000 at 31.7 Mgal/d. The large decreases in water use from 1985 to 1990 and again from 2005 to 2010 are primarily attributable to declines in groundwater withdrawals for rice irrigation from 10 Mgal/d in 1985 to 2.22 Mgal/d in 1990 and from 10.52 Mgal/d in 2005 to 5.14 Mgal/d in 2010. Surface-water withdrawals for general irrigation declined from 2.44 Mgal/d in 1985 to 0.42 Mgal/d in 1990 and from 2.2 Mgal/d in 2005 to 1.1 Mgal/d in 2010. Surface-water withdrawals for rice irrigation declined from 1.41 Mgal/d in 1985 to 0.66 Mgal/d in 1990 and from 2.06 Mgal/d in 2005 to 1.01 Mgal/d in 2010.

Water resources of Morehouse Parish, Louisiana

Released June 06, 2019 07:56 EST

2019, Fact Sheet 2018-3068

Vincent E. White

Information concerning the availability, use, and quality of water in Morehouse Parish, Louisiana, is critical for proper water-supply management. The purpose of this fact sheet is to present information that can be used by water managers, parish residents, and others for stewardship of this vital resource. In 2014, 109.84 million gallons per day (Mgal/d) of water were withdrawn in Morehouse Parish: 78.05 Mgal/d from groundwater sources and 31.79 Mgal/d from surface-water sources. Withdrawals for agricultural use—including general irrigation, rice irrigation, and livestock—accounted for about 97 percent (106.29 Mgal/d) of the total water withdrawn. Other categories of use included public supply, rural domestic, and industrial. Water-use data collected at 5-year intervals from 1960 to 2010 and again in 2014 indicated that water withdrawals peaked in 1975 at 167.82 Mgal/d.

Nonlinearities in transmission dynamics and efficient management of vector-borne pathogens

Released June 05, 2019 15:34 EST

2019, Ecological Applications (29) 1-14

Howard S. Ginsberg, Jannelle Couret

Integrated Pest Management (IPM) is an approach to minimizing economic and environmental harm caused by pests, and Integrated Vector Management (IVM) uses similar methods to minimize pathogen transmission by vectors. The risk of acquiring a vector-borne infection is often quantified using the density of infected vectors. The relationship between vector numbers and risk of human infection is more or less linear when both vector numbers and pathogen prevalence in vectors are low, but the relationship is nonlinear when vector density and/or infection prevalence are high. Therefore, the density of infected vectors often does not accurately predict risk of human exposure to pathogens, and traditional estimates of % Control often overestimate the level of protection from infection resulting from management programs. We suggest a modified estimator, % Protection, which more accurately quantifies protection against human infection resulting from a management intervention. Cost-effectiveness of a management program is critical to protection of both public health and the environment, because the more efficiently available resources and funding are used, the fewer people get sick, and well-targeted efficient management programs minimize the need for poorly-targeted, expensive environmental interventions (e.g., broadscale pesticide applications) that tend to damage nontarget organisms and natural systems. Design of an efficient, cost-effective IVM program requires knowledge of the cost-effectiveness functions (the effectiveness of control methods at lowering vector bites and/or infection prevalence with different levels of application) of the various control methods to be applied. Alternative programs can be designed that optimize % Protection by integrating different control methods at different levels of investment, and environmental effects of these alternatives can be compared, allowing environmental considerations to be included explicitly in the decision process. IPM, IVM, and Adaptive Management share the characteristic that management decisions must be made with incomplete knowledge of the functioning of natural systems or the efficacies of interventions. IVM surveillance programs that assess the effects of individual control methods and of combinations of control methods on the numbers of vector bites and on infection prevalence in vectors, can increase knowledge of pathogen transmission dynamics and provide information to improve program effectiveness in subsequent applications.

Genetic tagging in the Anthropocene: Scaling ecology from alleles to ecosystems

Released June 05, 2019 14:33 EST

2019, Ecological Applications (29) 1-17

Clayton T Lamb, Adam T Ford, Michael Proctor, Andy Royle, Garth Mowat

The Anthropocene is an era of marked human impact on the world. Quantifying these impacts 51 has become central to understanding the dynamics of coupled human-natural systems, resource52 dependent livelihoods, and biodiversity conservation. Ecologists are facing growing pressure to 53 quantify the size, distribution, and trajectory of wild populations in a cost-effective and socially54 acceptable manner. Genetic tagging, combined with modern computational and genetic analyses, 55 is an under-utilized tool to meet this demand, especially for wide-ranging, elusive, sensitive, and 56 low-density species. Genetic tagging studies are now revealing unprecedented insight into the 57 mechanisms that control the density, trajectory, connectivity and human-wildlife conflict for 58 populations over vast spatial scales. Here we outline the application of, and ecological inferences 59 from, new analytical techniques applied to genetically-tagged individuals, contrast this approach 60 with conventional methods, and describe how genetic tagging can be better applied to address 61 outstanding questions in ecology. We provide example analyses using a long-term genetic 62 tagging dataset of grizzly bears in the Canadian Rockies. The genetic tagging toolbox is a 63 powerful and overlooked ensemble that ecologists and conservation biologists can leverage to 64 generate evidence and meet the challenges of the Anthropocene.

Effect of amphibian chytrid fungus (Batrachochytrium dendrobatidis) on apparent survival of frogs and toads in the western USA

Released June 05, 2019 14:20 EST

2019, Biological Conservation (236) 296-304

Robin E. Russell, Brian J. Halstead, Brittany Mosher, Erin L. Muths, Michael J. Adams, Evan H. Campbell Grant, Robert N. Fisher, Patrick M. Kleeman, Adam R. Backlin, Christopher Pearl, R. Ken Honeycutt, Blake R. Hossack

Despite increasing interest in determining the population-level effects of emerging infectious diseases on wildlife, estimating effects of disease on survival rates remains difficult. Even for a well-studied disease such as amphibian chytridiomycosis (caused by the fungus Batrachochytrium dendrobatidis [Bd]), there are few estimates of how survival of wild hosts is affected. We applied hierarchical models to long-term capture-mark-recapture data (mean = 10.6 yrs, range = 6–15 yrs) from >5500 uniquely-marked individuals to estimate the effect of Bd on apparent survival of four threatened or endangered ranid frog species (Rana draytonii, R. muscosa, R. pretiosa, R. sierrae) at 14 study sites in California and Oregon (USA) and one bufonid toad (Anaxyrus boreas) at two study sites in Wyoming and Montana. Our models indicated that the presence of Bd on an individual reduced apparent survival of ranid frogs by ~6–15% depending on species and sex. The estimated difference between toads with and without Bd was 19% for the Montana population and 55% for the Wyoming population; however, the 95% Credible Interval of these estimates included zero. These results provide evidence for negative effects of Bd on survival in wild populations even in the absence of obvious die-offs. Determining what factors influence the magnitude of the effects of Bd on wildlife populations is an important next step toward identifying management actions. These estimates of Bd effects are important for understanding the extent and severity of disease, whether disease effects have changed over time, and for informing management actions.

Evaluation of land subsidence and ground failures at Bicycle Basin, Fort Irwin National Training Center, California, 1992–2017

Released June 05, 2019 08:40 EST

2019, Scientific Investigations Report 2019-5015

Jill Densmore, Kevin M. Ellett, Michelle Sneed, Justin T. Brandt, James F. Howle, Andrew Y. Morita, Rodrigo Borela, Antonio Bobet, Daniel C. Thayer

Groundwater has been pumped in the Bicycle Basin at Fort Irwin National Training Center since the 1960s, and the amount pumped has generally increased since the 1990s. After a large crack (approximately 0.5-kilometer long) formed at the surface of Bicycle Lake playa during 2005–06 in the area used as an aircraft runway, a monitoring study was initiated by the U.S. Geological Survey, in cooperation with the U.S. Army Fort Irwin National Training Center, to help determine the cause. The extent and effect of groundwaterlevel declines and land-surface deformation in Bicycle Basin were evaluated using a number of approaches, including water-level measurements from December 2007 to June 2017, land surveys across the playa area, interferometric synthetic aperture radar (InSAR) analyses, geophysical surveys of the playa area, and numerical experiments to test hypotheses about soil mechanical processes. A specific objective of this study was to evaluate the recent development of ground failures in the form of large, surface cracks that pose a hazard to aircraft operations on the Bicycle Lake playa airstrip.

Another large crack and set of interconnected cracks formed at the surface of Bicycle Lake playa in 2013 following a period of inundation similar to that of 2005–06; however, the 2013 cracks formed a network rather than a single feature. Groundwater pumping resulted in more than 27 meters (90 feet) of water-level declines in wells north of the Bicycle Lake playa from 1990 to 2017, and InSAR interferograms indicated more than 400 millimeters (16 inches) of subsidence during 1993–2015. Subsidence rates calculated from InSAR interferograms were variable, temporally and spatially. Results of leveling surveys indicated differential subsidence between 2009 and 2016 along a transect across the playa to the area of maximum subsidence; there was less subsidence south of the 2005–06 crack than north of it. The steepest subsidence gradient for this time was in the area of maximum subsidence. Repeat tape-extensometer measurements from April 2009 to November 2017 across the main-runway crack indicated slight opening along part of the crack. A baseline lidar (light detection and ranging) survey of the main-runway crack was done in January 2009 to track the development of this feature. During the 95-months from January 2009 to December 2016, 0.5 meters (19.7 inches) of subsidence was observed next to the subsidence pit in the crack along the western end of the scanned area, presumably due to erosion and backfilling when the lake was inundated. Standing water in the crack along the eastern end of the scanned area prevented determining change for that part of the crack. Time-series, shaded-relief images show the progression of change in the crack from January 2009 through December 2016, with the crack closing and opening, depending on the time of most recent inundation relative to when the scans were taken. Volumetric changes in the size of the crack, calculated between the sequential lidar surveys, show that from 2009 to 2016, the cumulative volumetric change was 1.5 cubic meters (54 cubic feet). This volume is a minimum estimate because the crack volume below the water surface in the pits was not included in the calculations. Subsurface imaging of the 2005–06 main-runway crack by a series of electrical resistivity tomography surveys in 2008 and 2017 indicated that the crack could extend 5 meters (16 feet) in the subsurface.

Electromagnetic induction surveys in 2008, 2014, and 2015 evaluated the technique for ground-failure monitoring and showed that the technique was effective at revealing anomalies correlated with the features of concern in the playa area, such as the 2005–06 crack, numerous ”healed” macropolygon features, and scattered sink-like depressions.

Results from numerical experiments simulating watertable decline at depth indicated that the material deposits in the desaturating capillary fringe zone might not be able to transmit large enough stresses up through the overlying soil to cause cracks at the land surface. Results from simulations of desiccation in the presence of a regional tectonically induced stress field, however, tended to support the hypothesis that the combined processes could control the formation of giant desiccation macropolygons in certain areas, such as Bicycle Lake playa.

Gap Analysis Project (GAP) Terrestrial Vertebrate Species Richness Maps for the Conterminous U.S.

Released June 04, 2019 16:30 EST

2019, Scientific Investigations Report 2019-5034

Kevin J. Gergely, Kenneth G. Boykin, Alexa J. McKerrow, Matthew J. Rubino, Nathan M. Tarr, Steven G. Williams

The mission of the Gap Analysis Project (GAP) is to support national and regional assessments of the conservation status of vertebrate species and plant communities. This report explains conterminous United States species richness maps created by the U.S. Geological Survey for four major classes in the phylum Chordata: mammals, birds, reptiles, and amphibians. In this work, we focus on terrestrial vertebrate species and the spatial patterns of richness derived from species’ habitat distribution models. We created species’ habitat distribution models for 1,590 species (282 amphibians, 621 birds, 365 mammals, 322 reptiles) and an additional 129 subspecies (2 amphibians, 28 birds, 94 mammals, 5 reptiles) that occur in the conterminous United States. The 1,590 species level models were spatially combined to create the taxa richness maps at a spatial resolution of 30 meters. Based on those maps we identified the maximum species richness for each of the taxa (43 amphibians, 163 birds, 72 mammals, and 54 reptiles) and show variation in richness across the conterminous United States. Because these habitat models remove unsuitable areas within the range of the species, the patterns of richness presented here are different from the coarse-resolution species’ habitat distribution models commonly presented in the literature. These maps provide a new, more spatially refined richness map. In addition, since these models are logically linked to mapped data layers that constitute habitat suitability, this suite of data can provide an intuitive data system for further exploration of biodiversity and implications for change at ecosystem and landscape scales.

Distribution of adult Chinook salmon (Oncorhynchus tshawytscha) in relation to water temperatures, Lake Scanewa, Cowlitz River, Washington, 2012

Released June 04, 2019 12:10 EST

2019, Open-File Report 2019-1055

Tobias J. Kock, Brian K. Ekstrom, Theresa L. Liedtke

A trap-and-haul program is operated to move anadromous Pacific salmon (Oncorhynchus spp.) around dams and reservoirs in the Cowlitz River basin, Washington. The primary release site for adult fish is in Lake Scanewa, a small reservoir created by Cowlitz Falls Dam, the uppermost dam in the basin. Releases in the reservoir are terminated when reservoir water temperature is 16 degrees Celsius (°C) or greater to reduce the risk of exposing adult salmon and steelhead (O. mykiss) to thermal conditions known to be stressful for these species. When the water temperature limit is reached, fish are released into the Cowlitz and Cispus Rivers upstream of the reservoir. Concerns have been raised about fish presence in the reservoir during warm conditions, so an empirical evaluation of water temperatures selected by spring Chinook salmon (O. tshawytscha) in Lake Scanewa was requested by resource managers. We conducted the evaluation during June–October 2012. Water temperature in the reservoir was measured using a series of thermographs combined with daily measurements at the Cowlitz Falls Fish Facility. Temperature-use data were collected from 50 adult hatchery-origin spring Chinook salmon tagged with temperature-sensing radio transmitters and released into the reservoir. This approach yielded a total of 930,056 individual temperature-use records in the reservoir during the study. Tagged fish occupied water temperatures less than 16 °C during most of the study period. Water temperatures ranged from 5 to 18.5 °C during the study, peaking in mid-August. Overall, about 25 percent of the detections of tagged fish were in water temperatures in the 16–20 °C range. In August, tagged fish detections in the 18–20 °C range comprised 13 percent of the total detections, and the remainder of the detections were in water less than or equal to 17 °C. Results from the study indicate that adult hatchery-origin spring Chinook salmon were able to locate and use water temperatures in the reservoir less than levels associated with stress. However, we also observed that thermal conditions in the reservoir were cool relative to most other years during 2008–16. Additional research may be warranted to better understand thermal exposure of adult spring Chinook salmon during warmer years.

Geological and geophysical data for a three-dimensional view—Inside the San Juan and Silverton Calderas, Southern Rocky Mountains Volcanic Field, Silverton, Colorado

Released June 04, 2019 11:10 EST

2019, Fact Sheet 2019-3026

Douglas B. Yager, Eric D. Anderson, Maria Deszcz-Pan, Bruce D. Smith, Brian D. Rodriguez


The San Juan-Silverton caldera complex located near Silverton, Colorado, in the Southern Rocky Mountains volcanic field is an ideal natural laboratory for furthering the understanding of shallow-to-deep volcanic-related mineral systems. Recent advances in geophysical data processing and three-dimensional (3D) model construction will help to characterize shallow properties important for understanding surface water and groundwater quality issues and will also improve knowledge of deep geological structures that may have been conduits for hydrothermal fluids that formed mineral deposits. The study has general applications to mineral resource assessments in other areas of the world and to identifying possible groundwater flow paths and associated geochemistry important in abandoned mine lands cleanup.

Silverton, Colorado, is the site of a spectacular succession of igneous rocks that formed beginning about 35 million years ago (Ma). Base metals (copper, lead, and zinc) and precious metals (silver and gold) mined from the late 1870s to 1991 owe their existence to a 25-million-year cycle of igneous activity. The presence of economic, base, and precious metal deposits within a complex geological setting were largely responsible for stimulating studies by the U.S. Geological Survey (USGS) conducted during the early 20th century. The focus of investigations in the late 20th and 21st centuries have broadened in scope to include abandoned mine lands (AML) investigations. The legacy of hard rock mining in headwater catchment areas caused environmental challenges for local communities and downstream water resource users. The Gold King Mine, located a few kilometers north of Silverton, illustrates the potential environmental effects of abandoned mines. On August 5, 2015, during reclamation efforts at the Gold King Mine, a breach of collapsed workings sent approximately 3 million gallons of acidic and metal-rich mine water into the upper Animas River, a tributary to the Colorado River Basin. Mining-related sources of metals and acidity add to geological sources of metals in surface water and groundwater. Weathering processes of altered and mineralized rock have been a source of acid rock drainage that have been ongoing for millennia.

Contemporary human impacts on alpine ecosystems: the direct and indirect effects of human-induced climate change and land use

Released June 04, 2019 08:57 EST

2019, Book chapter, Reference Module in Earth Systems and Environmental Sciences

Daniel E. Winkler

Alpine ecosystems account for ca. 3 % of terrestrial habitats yet, along with adjacent mountain systems, provide water resources to nearly half of the world’s human population. Approximately 20 % of humans live in or near mountain areas, making it inherently important to understand current impacts on these systems. Here, I review literature regarding current and projected human impacts on alpine ecosystems, including the direct and indirect impacts of human-induced climate change on alpine plant, animal, and soil communities. I also discuss the influence of recreation and tourism, grazing, and other land use changes including the introduction of non-native and invasive species in alpine systems. I conclude with management implications as well as future areas of research needed to better understand changes to these systems.

Petrology of volcanic rocks associated with silver-gold (Ag-Au) epithermal deposits in the Tonopah, Divide, and Goldfield Mining Districts, Nevada

Released June 03, 2019 13:15 EST

2019, Scientific Investigations Report 2019-5024

Edward A. du Bray, David A. John, Joseph P. Colgan, Peter G. Vikre, Michael A. Cosca, Leah E. Morgan

Miocene calc-alkaline volcanic rocks, part of the southern segment of the ancestral Cascades magmatic arc, are spatially, temporally, and likely genetically associated with precious metal epithermal deposits in the Tonopah, Divide, and Goldfield Districts of west-central Nevada. In the Tonopah mining district, volcanic rocks include the Mizpah Trachyte, Fraction Tuff, and Oddie Rhyolite; in the Divide mining district, they include the Heller Tuff, Brougher Rhyolite, trachyandesite of Red Mountain, Divide Andesite, and volcanics of Donovan Peak (which includes rhyolite, dacite, and rhyodacite units); in the Goldfield mining district they include the Milltown Andesite, an unnamed porphyritic andesite, and latite. All these rocks are porphyritic and contain phenocryst assemblages that include plagioclase, pyroxene, hornblende, biotite, quartz, alkali feldspar, and olivine. These mostly subalkaline, metaluminous, calc-alkalic, and magnesian rocks range from basaltic trachyandesite to rhyolite and contain 54 to 78 weight percent silicon dioxide.

In the Divide mining district, the Divide Andesite and the volcanics of Donovan Peak are compositionally distinct from volcanic rocks in the other two mining districts. These rocks define a somewhat more restricted range of silicon dioxide content; are more alkalic; have greater titanium dioxide, sodium oxide, barium, hafnium, lanthanum, niobium, tantalum, yttrium, ytterbium, and zirconium abundances; and lower magnesium oxide, strontium, and vanadium abundances. Elevated zirconium contents are particularly characteristic of these rocks, which are also distinctly younger than most of the rocks in the other two mining districts. The alkalic character (principally higher sodium oxide abundances) and elevated zirconium contents characteristic of the Divide Andesite and the volcanics of Donovan Peak suggest that distinctive sources and (or) processes contributed to the petrogenesis of these rocks.

In the Tonopah, Divide, and Goldfield mining districts the geochemistry of Oligocene and Miocene volcanic rocks constrain the processes that contributed to the petrogenesis of these rocks. Specifically, major oxide compositional variation among these rocks is consistent with crystallization and fractionation of the observed phenocryst minerals. In addition, these rocks have negatively sloping rare-earth element patterns consistent with partial melting in a high-pressure, garnet stable regime. Elevated strontium concentrations and small negative europium anomalies are consistent with partial melting in a plagioclase-unstable setting. However, larger negative europium anomalies among the more silica-rich volcanic rocks indicates a progressively greater role for plagioclase fractionation among these rocks. The importance of hornblende in the petrogenesis of these rocks is reflected in subtly U-shaped middle rare-earth element pattern segments. Increasing lead/cerium and decreasing phosphorus pentoxide/potassium oxide with increasing silicon dioxide are characteristic of these volcanic rocks. These characteristics and their distinctive pre-Cenozoic xenolith content suggest a significant role for crustal contamination in their petrogenesis. Diagnostic textural features preserved by phenocrysts, especially plagioclase, constitute additional evidence that open-system behavior, including reservoir-scale mixing, recharge, and assimilation, was critical to the petrogenesis of volcanic rocks in the Tonopah, Divide, and Goldfield mining districts.

The National Map—New data delivery homepage, advanced viewer, lidar visualization

Released June 03, 2019 12:49 EST

2019, Fact Sheet 2019-3032

U.S. Geological Survey

As one of the cornerstones of the U.S. Geological Survey’s (USGS) National Geospatial Program, The National Map is a collaborative effort among the USGS and other Federal, State, and local partners to improve and deliver topographic information for the Nation. The National Map is featuring direct links to new and improved GIS data access utilities on a refreshed data delivery homepage at https://www.usgs.gov/NationalMap/data. From the homepage, users can now quickly access topographical map products, GIS data, and the full suite of The National Map’s applications and visualization services.

Ecological islands: Conserving biodiversity hotspots in a changing climate

Released June 03, 2019 09:35 EST

2019, Frontiers in Ecology and the Environment

Jennifer M. Cartwright

For decades, botanists have recognized that rare plants are clustered into ecological “islands”: small and isolated habitat patches produced by landscape features such as sinkholes and bedrock outcrops. Insular ecosystems often provide unusually stressful microhabitats for plant growth (eg because of thin soils, high temperatures, extreme pH, or limited nutrients) to which rare species are specially adapted. Climate-driven shifts to these stressors may undermine the competitive advantage of stress-adapted species, allowing them to be displaced by competitors, or may overwhelm their coping strategies altogether. Special features of insular ecosystems—such as extreme habitat fragmentation and association with unusual landscape features—may also affect their climate sensitivity and adaptive capacity. To predict and manage these changes, a simple conceptual framework is presented based on a synthesis of over 300 site-level studies. Using this framework, conservation efforts can leverage existing ecological knowledge to anticipate changes in particular microhabitats and design targeted strategies for conserving rare species.

An ANCOVA model for porosity and its uncertainty for oil reservoirs based on TORIS dataset

Released June 02, 2019 14:23 EST

2019, Journal of Petroleum Science and Engineering

Cevat (Ozgen) Karacan

Porosity is one of the most important parameters to assess in-place oil or gas in reservoirs, and to evaluate recovery from enhanced production operations. Since it is relatively well-established to determine porosity using different laboratory and field methods, its value is usually determined at many locations across a reservoir as part of the common practice to capture reservoir heterogeneity and the variability in values. This suite of measurements and the distribution of values are most valuable for probabilistic reservoir assessments, and for spatial modeling if the exact data locations are known.

Despite the importance of individual measurements to set the range of values for probabilistic studies, it is not always possible to access these data due to confidentiality. In most cases, commercial or publicly available databases that assessments may rely on usually report only mean values of porosity, like any other reservoir data, or they may not report a value at all. This makes both quantifying the mean value and the uncertainty around it difficult for probabilistic assessments.

In this study, the TORIS (Tertiary Oil Recovery Information System) dataset of the National Petroleum Council and the U.S. Department of Energy was used to model porosity and the uncertainty around predicted values. TORIS is an integrated dataset of production data, reservoir properties, and project databases of crude oil reservoirs in the United States. The model presented in the paper was based on ANCOVA (Analysis of Co-Variance) of data from 1038 reservoirs from the TORIS dataset for porosity prediction, validation and testing for quantitative and qualitative parameters that may be readily available in most cases, and to estimate uncertainty around the mean values. This model also explored association of porosity values to different parameters, and to different depositional systems and diagenetic overprint conditions. Furthermore, an ANN (Artificial Neural Network) model was created to compare the predicted values of both models. Results showed that the ANN model was able to represent more of the variability, however it lacked the insights that might be gained from the ANCOVA model.

User needs for future Landsat missions

Released June 01, 2019 09:42 EST

2019, Remote Sensing of Environment

Zhuoting Wu, Gregory Snyder, Carolyn M. Vadnais, Rohit Arora, Michael Babcock, Gregory L. Stensaas, Peter Doucette, Timothy Newman

Landsat satellites have been operating since 1972, providing the longest continuous observation record of the Earth’s land surface. Over the past half century, the Landsat user community has grown exponentially, encompassing more diverse and evolving scientific research and operational uses. Understanding current and future user needs is crucial to informing the design of Landsat missions beyond Landsat 9. The U.S. Geological Survey (USGS) initiated a user needs collection process to document needs from U.S. Federal civil subject matter experts who rely on moderate-resolution land imaging data across a diverse range of scientific research and application domains. In total, 379 moderate-resolution land imaging user needs were collected through structured interviews. The findings indicate that, at present, users need continuity in Landsat capabilities with free and open data access. Improvements to future Landsat systems should include 10 m spatial resolution and at least weekly cloud-free observation frequency. Spectral enhancements should include the addition of red edge bands, and multiple, narrower visible, near infrared, shortwave infrared, and thermal infrared bands. Ideally, a variety of applications need continuous, full-spectrum coverage in 10 nm-wide bands spanning the visible to shortwave infrared (VSWIR) region (400–2500 nm) and 5 to 8 multispectral thermal infrared bands. Non-Federal (state, local, commercial, academic, and international) sources found similar results, but a more comprehensive comparison across these communities through a broader survey may provide additional insights. USGS-collected moderate-resolution land imaging user needs are an input to the Landsat 10 Architecture Study to develop and assess feasible Landsat 10 mission architectures.

Wild canid distribution and co-existence in a natural–urban matrix of the Pioneer Valley of Western Massachusetts

Released May 31, 2019 16:00 EST

2019, Northeastern Naturalist (26) 325-342

Eric G. LeFlore, Todd K. Fuller, John T. Finn, John F. Organ, Stephen DeStefano

Although development and urbanization are typically believed to have negative impacts on carnivoran species, some species can successfully navigate an urban matrix. Sympatric carnivorans compete for limited resources in urban areas, likely with system-specific impacts to their distributions and activity patterns. We used automatically triggered wildlife cameras to assess the local distribution and co-existence of Canis latrans (Coyote), Vulpes vulpes (Red Fox), and Urocyon cinereoargenteus (Gray Fox) across the Pioneer Valley, MA, in relation to different levels of human development. We placed cameras at 79 locations in forested, altered, and urban land-use areas from September to November 2012 and accumulated 1670 trap nights. We determined site characteristics and detection rates for 12 other wildlife species for each camera location to develop a generalized linear model for the local distribution of each focal canid species across the study area. We also compared diel activity patterns among Coyotes, Red Foxes, and Gray Foxes, and calculated coefficients of overlap between each pair. The local distribution of Coyotes was positively associated with the detection rates of their prey and not associated with detection rates of sympatric carnivoran species. Red Foxes and Gray Foxes had negative relationships with the detection rate of Coyotes, and none of the 3 canid species showed a positive correlation with increased levels of urbanization. There was a high degree of temporal overlap in diel activity patterns and limited spatial overlap of our focal species, which suggests that any competition avoidance across our study area occurred at the spatial level. Coyotes fill the role of top predator in the Pioneer Valley, and likely have a negative impact on the local distributions of smaller canids, while their own local distributions seem to be driven by prey availability.

Monitoring five-needle pine on Bureau of Land Management lands in Wyoming summary report for 2013, 2014, 2016, 2017

Released May 31, 2019 15:27 EST

2019, Report

Erin Shanahan, Kristin Legg, Rob Daley, Kathryn Irvine, Siri Wilmoth, Joshua Jackson

Whitebark pine (Pinus albicaulis) grows at high elevations and in subalpine communities in the Pacific Northwest and Northern Rocky Mountains. Limber pine (Pinus flexilis) occurs in western North America across a broad elevational gradient from the Canadian Rocky Mountains into parts of New Mexico and Arizona and from southern California eastward to the few, isolated populations existing on the western boundary of the Dakotas and Nebraska (Steele 1990, Schoettle and Rochelle 2000). Both of these five-needle pine species play a variety of ecological roles and are considered key components in the their environments. Currently, whitebark pine and limber pine are being impacted by multiple ecological disturbances. White pine blister rust, caused by the introduced fungus Cronartium ribicola, mountain pine beetle (Dendroctonus ponderosae), dwarf mistletoe (Arceuthobium spp.), wildfires, and drought all pose significant threats to the persistence of healthy five-needle populations. An effort was initiated in 2013 by the National Park Service and the Wyoming Bureau of Land Management (WYBLM) to evaluate and monitor the long-term health trajectory of five-needle pines on WYBLM lands within the Greater Yellowstone Ecosystem (GYE). With guidance from the Interagency Whitebark Pine Monitoring Program protocol, and employing a rapid assessment survey technique specifically designed for this endeavor, we monitored whitebark pine trees in 2013, 2014, 2016, 2017. We estimated the proportion of live, five-needle pine trees (>1.4 m tall) infected with white pine blister rust, documented blister rust infection severity by the occurrence and location of persisting and new infections, determined mortality of five-needle pine trees and described potential factors contributing to the death of trees, and assessed the multiple components of recruitment of understory five-needle pine into the reproductive population. White pine blister rust was widespread throughout WYBLM lands within the GYE. Using a combined ratio estimator we found that the proportion of live, >1.4 m tall five-needle pine trees infected with white pine blister rust was 0.156 (±0.054 SE; this estimate combines all surveyed trees). Bole cankers were 25% more prevalent than branch cankers in all five-needle pines observed. Mortality of surveyed trees on WYBLM lands was predominantly attributed to mountain pine beetle. For seedlings and saplings, a total of 4003 live, ≤1.4 m tall five-needle pines were documented. Cones or cone scars were recorded on 745 of the live trees. Of these reproducing trees, 44 were recorded with white pine blister rust infection. Long-term monitoring on five-needle pines on WYBLM lands will continue into the future.

Guidance for assessing interregional ecoystem service flows

Released May 30, 2019 16:24 EST

2019, Ecological Indicators (105) 92-106

Thomas Koellner, Aletta Bonn, Sebastian Arnhold, Kenneth J. Bagstad, Dor Friedman, Carlos Guerra, Thomas Kastner, Meidad Kissinger, Janina Kleeman, Christian Kuhlicke, Jianguo Liu, Laura Lopez-Hoffman, Alexandra Marques, Berta Martin-Lopez, Catharina J. E. Schulp, Sarah Wolff, Matthias Schröter

Ecosystem services (ES) assessments commonly focus on a specific biophysical region or nation and take its geographic borders as the system boundary. Most geographical regions are, however, not closed systems but are open and telecoupled with other regions through ES imports and exports, which are mediated by fluxes of matter, energy and information. Interregional ES flows are often linked to national economies and may affect issues of national security and global equity. To date, however, methodologies for interregional ES flow assessments have been published in dispersed literature. This paper provides a three-step guidance for the assessment of four different types of interregional ES flows (traded goods, passive biophysical flows, species migration and dispersal and information flows), in order to complement national ecosystem assessments. The three steps are to (i) define the goal and scope of interregional ES flow assessments, (ii) quantify the interregional ES flows using a tiered approach and (iii) interpret results in terms of uncertainties, consequences and governance options. We compile different indicators for assessing interregional ES flows and evaluate their suitability for national ES assessments. Finally, in order to value the various outcomes of telecouplings, including their implications for human well-being, we relate the interregional ES flow indicators to the Sustainable Development Goals. We discuss how regional studies can assess a country‘s dependence and impact on "overseas" ES. This guidance towards systematic assessment of interregional ES flows provides a first step to measure and quantify externalised environmental costs and can contribute to the development of indicators to address interregional imbalances in trade, foreign policy and beyond.

Managing the trifecta of disease, climate, and contaminants: Searching for robust choices under multiple sources of uncertainty

Released May 30, 2019 15:36 EST

2019, Biological Conservation (236) 153-161

Kelly Smalling, Collin Eagles-Smith, Rachel A. Katz, Evan Grant

Wood frogs, like other amphibian species worldwide, are experiencing population declines due to multiple stressors. In the northeastern United States, wood frog declines are thought to result from a reduction in successful metamorphosis in part due to climate change, disease (specifically ranavirus) and contaminant exposure. The presence of multiple stressors can increase uncertainty in characterizing the main effects of each stressor, as well as understanding the degree to which their effects interact (additively or synergistically) to impact populations. This uncertainty adds inherent challenges to selecting appropriate management actions for conserving populations. Finding solutions that are robust to these uncertainties can improve management amid absent or equivocal knowledge. We used a Bayesian Belief Network (BBN), a quantitative tool that allowed us to evaluate how potential management actions might mitigate the effects of increasingly frequent and severe droughts, ranavirus exposure, and methylmercury on wood frog populations in the northeastern US. In our system, successful wood frog recruitment was largely driven by hydroperiod regardless of other stressors. Our modelling indicated that increased hydroperiod lowered the probability of complete metamorphosis failure from 0.6 to 0.37, suggesting that under the conditions tested in the model, pond hydrology, is more important for successful recruitment than either methylmercury or ranavirus exposure. As more information becomes available on stressor interactions, model scenarios could be re-run and management options re-evaluated.

Methane and nitrous oxide temporal and spatial variability in two midwestern USA streams containing high nitrate concentrations

Released May 30, 2019 09:51 EST

2019, Science of the Total Environment (685) 574-588

Richard L. Smith, John K. Böhlke

Concentrations and emissions of greenhouse gases CO2, CH4, and N2O commonly are examined individually in aquatic environments in which each is expected to be relatively important; however, their co-occurrence and dynamic interactions in fluvial settings could provide important information about their controlling biogeochemical processes and potential contributions to global climate change. Spatial and temporal variability of CH4, N2O, and CO2 concentrations were measured from June 1999 to September 2003 in two nitrate-rich (40–1200 μM) streams draining agricultural land in the midwestern USA that differed ~13-fold in flow. Seasonal (biweekly), diel (hourly), and transport-oriented (reach-scale) sampling approaches were compared. Dissolved gas concentrations exceeded atmospheric equilibrium values up to 700- and 16-fold, for CH4 and N2O, respectively. Mean concentrations were higher in the larger stream than in the smaller stream. In both streams, CH4 emissions were generally higher in summer-fall and negatively correlated with flow and NO3 concentration while N2O emissions were generally higher in winter/spring and positively correlated with flow and NO3. In the small stream, diel variations in the concentrations, emissions, and isotopic compositions of CH4, N2O, and NO2 resulted from diel variations in sources, sinks, and air-water gas exchange velocities. Seasonal mean total (CH4 + N2O) area-normalized emission rates, expressed as CO2 warming potential equivalents, were similar for the two streams, but the total reach-scale emission rate for the larger stream, including CO2, was about 2.9 times that of the smaller stream (131.6 vs 46.0 kg CO2 equivalents km−1 day−1, respectively). The CH4contribution to this flux was 9–28%, despite the relatively high NO3and O2 concentrations in the streams, indicating contributions from upwelling groundwater or reactions in streambed sediment.

Early genetic outcomes of American black bear reintroductions in the Central Appalachians, USA

Released May 29, 2019 15:48 EST

2019, Ursus (29) 110-133

Sean M. Murphy, John T. Hast, Ben C. Augustine, David W. Weisrock, Joseph D. Clark, David. M Kocka, Christopher W. Ryan, Jaime L. Sajecki, John J. Cox

Habitat loss and overexploitation extirpated American black bears (Ursus americanus) from most of the Central Appalachians, USA, by the early twentieth century. To attempt to restore bears to the southwestern portion of this region, 2 reintroductions that used small founder groups (n = 27 and 55 bears), but different release methods (hard versus soft), were conducted during the 1990s. We collected hair samples from black bears in the reintroduced Big South Fork (BSF) and Kentucky–Virginia populations (KVP), their respective Great Smoky Mountains (GSM) and Shenandoah National Park (SNP) source populations, and a neighboring population in southern West Virginia (SWV) to investigate the early genetic outcomes of bear reintroduction. Despite having undergone genetic bottlenecks, genetic diversity remained similar between reintroduced populations and their sources ~15 years after the founder events (ranges: AR = 4.86–5.61; HO = 0.67–0.75; HE = 0.65–0.71). Effective population sizes of the reintroduced KVP and BSF (NE = 31 and 36, respectively) were substantially smaller than their respective SNP and GSM sources (NE = 119 and 156, respectively), supporting founder effects. Genetic structure analysis indicated that the hard released (i.e., no acclimation period) KVP founder group likely declined considerably, whereas the soft released BSF founder group remained mostly intact, suggesting superior effectiveness of soft releases. Asymmetrical gene flow via immigration from the SWV has resulted in the KVP recovering from the initial founder group reduction. Sustained isolation, small NE, and small population size of the BSF may warrant continued genetic monitoring to determine if gene flow from neighboring populations is established or NE declines. For future bear reintroductions, we suggest managers consider sourcing founders from populations with high genetic diversity and soft-releasing bears to locales that are, if possible, within the dispersal capability of extant populations to mitigate the potential consequences of founder effects and isolation.

The influence of body size, condition, and age on recruitment of four Alaskan brown bear populations

Released May 29, 2019 15:06 EST

2019, Ursus (2) 111-118

Grant V. Hilderbrand, David Gustine, Kyle Joly, Buck Mangipane, William Leacock, Matthew Cameron, Mathew Sorum, Lindsey Mangipane, Joy Erlenbach

Recruitment of brown bear (Ursus arctos) offspring into a population is the product of initial cub production and subsequent survival and is a critical component of overall population status and trend. We investigated the relationship between maternal body size, body condition, and age (as a surrogate for gained experience) and recruitment of dependent offspring (≥1 yr old) in 4 Alaska, USA (2014–2017), brown bear populations using logistic regression. Body size alone was our top predictor of the presence of offspring and appeared in all top models. Our data suggest that bear size is the primary driver of productivity across all 4 study populations, with larger bears having a greater chance of being observed with offspring. The effect of body condition was likely confounded by the increased energetic costs of supporting cubs through time and had a negative relationship with recruitment. Age (experience) was positively related to recruitment. Understanding the relative importance of body size, body condition, and age on the recruitment of offspring provides insights into life-history trade-offs female bears must manage as they strive to meet the nutritional costs of cub production and rearing, while minimizing risks to themselves and their offspring. Further assessment of long-term longitudinal studies of brown bears that assess the lifetime reproductive output of individuals would be highly informative to further assess the effect of experience on recruitment and to support the management of brown bear populations for recovery, conservation, sustained yield, and ecosystem function.

Simulation of groundwater flow in the Brunswick Area, Georgia, for 2004 and 2015, and selected groundwater-management scenarios

Released May 29, 2019 11:15 EST

2019, Scientific Investigations Report 2019-5035

Gregory S. Cherry

The Upper Floridan aquifer (UFA) is the principal water source for industrial and public supply in Glynn County, Georgia. Wells in active pumping centers that tap the UFA for industries near the city of Brunswick have created an upward hydraulic-head gradient in the Floridan aquifer system, which has allowed high chloride (saline) groundwater from the Fernandina permeable zone of the Lower Floridan aquifer (LFA) to migrate upward into freshwater zones. Chloride concentrations of more than 250 milligrams per liter—the State and Federal secondary drinking-water standard—have been measured in a 2-square-mile area near downtown Brunswick.

An existing regional U.S. Geological Survey modular finite-difference groundwater-flow model (MODFLOW-2000) was modified using greater horizontal and vertical resolution to enable more detailed simulation of the effects of pumping in the vicinity of chloride contamination. Modifications to the regional model consisted of (1) limiting grid size to a maximum of 500 feet (ft) per side in the vicinity of the chloride plume; (2) representing the upper and lower Brunswick aquifers with distinct model layers; (3) similarly, representing upper and lower water-bearing zones of the UFA with distinct model layers in Glynn and Camden Counties, Ga.; and (4) establishing new hydraulic-property geographic zones in the UFA within Glynn County. The revised groundwater-flow model was calibrated to steady-state conditions that were assumed to exist during 2000 and 2004. The calibration and framework of the revised groundwater-flow model were documented in a separate report. For the current study, steady-state conditions were calibrated using October 2015 pumping rates in the Brunswick/Glynn County area as a 2015 Base Case. The 2015 Base Case simulation was used as the basis to evaluate seven groundwater-management scenarios in the Brunswick/Glynn County area.

Seven groundwater management-scenarios were developed on the basis of short- and long-term groundwater-use projections for the UFA in the Brunswick/Glynn County area. Scenarios A and B simulated additional pumping in the upper water-bearing zone (UWBZ) of the UFA at existing public-supply wells located near a chloride plume and planned public-supply wells to be constructed north of downtown Brunswick. Scenario C simulated a shutdown at Brunswick Cellulose Inc. and Pinova Inc. and the resulting deactivation of nine production wells, with a combined total pumping of 31.3 million gallons per day (Mgal/d) for the 2015 Base Case simulation. Scenario D (three scenarios) simulated 12.5, 25, and 50 percent (designated Scenarios D1, D2, and D3) of the total pumping of 31.3 Mgal/d at Brunswick Cellulose and Pinova. The objective of Scenario D was to determine pumping rates that may reverse groundwater-flow directions toward the Brunswick Cellulose well field and potentially allow groundwater with higher chloride concentration to migrate toward nearby public-supply wells. Scenario E simulated an additional pumping of 5 Mgal/d from the UWBZ of the UFA at a recently constructed production well within the Brunswick Cellulose well field.

Backward particle-tracking (MODPATH) analysis in public-supply wells located just outside the chloride plume to the north shows that predominant groundwater-flow directions are from the northeast toward the Brunswick Cellulose well field. The analysis covered 20- and 50-year periods for the 2015 Base Case and Scenario C simulations with 100 percent of backtracked particles remaining in the UWBZ and lower water-bearing zone of the UFA. Groundwater-flow directions are characterized by some vertical movement and dominant horizontal movement away from the chloride plume in the northern Brunswick area. For the 2015 Base Case simulation, the mean rate of particle movement ranged from 268 to 413 feet per year. For the Scenario C simulation, the mean rate of particle movement ranged from 89 to 182 feet per year with 50 percent of particles migrating from the chloride plume area. The rate of particle movement is influenced most by the horizontal hydraulic-head gradient in the UWBZ of the UFA.

The revised groundwater-flow model is subject to the limitations documented in the original model. In addition, the values used for the specified-head boundaries in the Floridan aquifer system for the 2004 calibrated model were based on the sparse data available and were not changed for the 2015 update to the model. These model boundaries control 80 percent of the inflows and about 60 percent of the outflows. Composite-scaled sensitivities of the model parameters indicate the revised model is most sensitive to pumping rates, followed by the horizontal hydraulic conductivity in the UFA for zones along coastal Georgia.

Simulation of the regional groundwater-flow system in the St. Louis River basin, Minnesota

Released May 29, 2019 11:15 EST

2019, Scientific Investigations Report 2019-5033

Megan J. Haserodt, Randall J. Hunt, Timothy K. Cowdery, Andrew T. Leaf, Anna C. Baker

The St. Louis River Basin (SLRB) covers 3,600 square miles in northeastern Minnesota, with headwaters in the Mesabi Range and extensive wetlands and lakes throughout the basin. To better understand the regional groundwater system in the SLRB, a two-dimensional, steady-state groundwater-flow model of the SLRB was developed by the U.S. Geological Survey, in cooperation with the Minnesota Ojibwe Bands, using the analytic-element computer code GFLOW. The parameter-estimation software suite PEST was used to obtain a best fit of the modeled to measured groundwater levels and streamflows. The calibrated regional model was locally refined to create a smaller version of the model, the central SLRB model, that was used to evaluate hydrologic effects from extensive ditching in wetlands of the central SLRB. The refinements included adding ditches that were not represented in the regional model and modifying the aquifer base elevation to be more representative of the localized area. The central SLRB model was recalibrated to better match the distribution of mapped wetlands. Two scenarios were run of the central SLRB model: one with ditches and one without ditches. The model results were compared between the two scenarios to assess the effect of ditching on the groundwater system and potential changes to hydrologic conditions that support wetlands.

Calibration of the regional SRLB model resulted in average horizontal hydraulic conductivity values of 6–39 feet per day for the glacial deposits and 3–4 feet per day for the uppermost fractured bedrock in the Biwabik Iron-Formation on the Mesabi Range. Average recharge across the calibrated model was 5.9 inches per year. Linesink resistance for the routed stream network was calibrated by using resistance categories based on the mapped soil hydrologic groups. The modeled regional groundwater-flow direction was generally to the south near the Mesabi Range topographic high and south or southwest across the rest of the basin.

The updated calibration of the central SLRB model resulted in average horizontal hydraulic conductivity values of 5–36 feet per day for the glacial deposits and 3 feet per day for the uppermost fractured Biwabik Iron-Formation of the Mesabi Range. Average recharge across the ditch scenarios was 4.1 inches per year. Comparison of the preditch and postditch model scenarios showed that ditching reduced the area where the modeled water table was within 1 foot of the land surface (a wetland hydrology indicator) in as much as 40,000 acres, or 37 percent, of mapped permanent wetlands in the SLRB. An increase in the depth to the water table in wetland areas has the potential to degrade wetland persistence or function.

The integrated monarch monitoring program: From design to implementation

Released May 29, 2019 09:21 EST

2019, Frontiers in Ecology and Evolution

Alison B Cariveau, Holly L Holt, James P Ward, Laura Lukens, Kyle Kasten, Jennifer Thieme, Wendy Caldwell, Karen Tuerk, Kristen A Baum, Pauline Drobney, Ryan G. Drum, Ralph Grundel, Keith Hamilton, Cindy Hoang, Karen Kinkead, Julie McIntyre, Wayne E. Thogmartin, Tenlea Turner, Emily L. Weiser, Karen Oberhauser

Steep declines in North American monarch butterfly (Danaus plexippus) populations have prompted continent-wide conservation efforts. While monarch monitoring efforts have existed for years, we lack a comprehensive approach to monitoring population vital rates integrated with habitat quality to inform adaptive management and effective conservation strategies. Building a geographically and ecologically representative dataset of monarchs and their habitat will improve these efforts. These data will help track long-term changes in the distribution and abundance of monarchs and their habitats, refine population and habitat models, and illuminate how conservation activities affect monarchs and their habitats. The Monarch Conservation Science Partnership developed the Integrated Monarch Monitoring Program (IMMP) to profile breeding habitats and their use by monarchs in North America. A spatially balanced random sampling framework guides site selection, while also allowing opportunistic inclusion of sites chosen by participants, such as conservation areas. The IMMP weaves new protocols together with those from existing monitoring programs to improve data compatibility for assessing milkweed (Asclepias spp.) density, nectar resources, monarch reproduction and survival, and adult monarch habitat use. Participants may select a protocol subset according to interests or local monitoring objectives, thereby maximizing contributions. Conservation partners, including public and private land managers, academic researchers, and citizen scientists contribute data to a national dataset available for analyses at multiple scales. We describe the program and its development, implementation elements that make the program robust and feasible, participation to date, and how IMMP data can advance research and conservation for monarchs, pollinators, and their habitats.

Groundwater quality in shallow aquifers in the western Mojave Desert, California

Released May 28, 2019 14:48 EST

2019, Fact Sheet 2019-3033

Krishangi D. Groover, Dara A. Goldrath

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The Priority Basin Project (PBP) of the GAMA Program provides a comprehensive assessment of the State’s groundwater quality and increases public access to groundwater-quality information. One GAMA-PBP study unit is in the western part of the Mojave Desert, where shallow aquifers provide drinking water for many rural households.

Effects of simple acid leaching of crushed and powdered geological materials on high-precision Pb isotope analyses

Released May 28, 2019 11:04 EST

2015, Geochemistry, Geophysics, Geosystems (16) 2276-2302

Erin Todd, Andreas Stracke, Erik Scherer

We present new results of simple acid leaching experiments on the Pb isotope composition of USGS standard reference material powders and on ocean island basalt whole rock splits and powders. Rock samples were leached with cold 6 N HCl in an ultrasonic bath, then on a hot plate, and washed with ultrapure H2O before sample digestion in HF‐HNO3 and chromatographic purification of Pb. Lead isotope analyses were measured by Tl‐doped MC‐ICPMS. Intrasession and intersession analytical reproducibilities of repeated analyses of both synthetic Pb solutions and Pb from single digests of chemically processed natural samples were generally better than 100 ppm (2 SD). The comparison of leached and unleached samples shows that leaching consistently removes variable amounts of contaminants that differ in Pb isotopic composition for different starting materials. For repeated digests of a single sample, analyses of leached samples reproduce better than those of unleached ones, confirming that leaching effectively removes most of the heterogeneously distributed extraneous Pb. Nevertheless, the external reproducibility of leached samples is still up to an order of magnitude worse than that of Pb solution standards (∼100 ppm). More complex leaching methods employed by earlier studies yield Pb isotope ratios within error of those produced by our method and at similar levels of reproducibility, demonstrating that our simple leaching method is as effective as more complex leaching techniques. Therefore, any Pb isotope heterogeneity among multiple leached digests of samples in excess of the external reproducibility is attributed to inherent isotopic heterogeneity of the sample. The external precision of ∼100 ppm (2 SD) achieved for Pb isotope ratio determination by Tl‐doped MC‐ICPMS is thus sufficient for most rocks. The full advantage of the most precise Pb isotope analytical methods is only realized in cases where the natural isotopic heterogeneity among samples in a studied suite is substantially below 100 ppm.

Growing pains of crowdsourced stream stage monitoring using mobile phones: The development of CrowdHydrology

Released May 28, 2019 09:46 EST

2019, Frontiers in Earth Science (7)

Christopher Lowry, Michael N. Fienen, Damon M. Hall, Kristine Stepenuck

Citizen science-based approaches to monitor the natural environment tend to be bimodal in maturity. Older and established programs such as the Audubon’s Christmas bird count and Community Collaborative Rain, Hail, and Snow Network (CoCoRaHS) have thousands of participants across decades of observations, while less mature citizen science projects have shorter lifespans often focused on local or regional observations with tens or hundreds of participants. For the latter, it can be difficult to transition into a more mature and sustainable citizen science-based research program. This paper focuses on this transition by evaluating CrowdHydrology (ca. 2010), a citizen science project that has transitioned from a regional to national network. It evaluates the data accuracy, citizen participation, and station popularity. The CrowdHydrology network asks citizens to send in text messages of water levels in streams and lakes, which has resulted in 16,294 observations submitted by over 8,000 unique participants at 120 unique locations. Using water level data and participation records from CrowdHydrology, we analyze the expansion and citizen participation from a regional to national citizen science network. We identify barriers to participation and evaluate why some citizen science observation stations are popular while others are not. We explore our chosen contributory program model for CrowdHydrology and the influence this model has had on long-term participation. Results demonstrate a highly variable rate of contributions of citizen scientists. This paper proposes hypotheses on why many of our observations are from one-time participants and why some monitoring stations are more popular than others. Finally, we address the future expansion of the CrowdHydrology network by evaluating successful monitoring locations and growing interest of watershed groups to expand the network of gauges.

Explosive summit collapse of Kīlauea Volcano in 1924 preceded by a decade of crustal contamination and anomalous Pb isotope ratios

Released May 28, 2019 09:38 EST

2019, Geochimica et Cosmochimica Acta (258) 120-137

Aaron Pietruszka, Daniel E. Heaton, Michael O Garcia, Jared P. Marske

A geochemical time-series analysis of lavas from frequently active basaltic volcanoes has the potential to reveal the enigmatic mantle controls on volcanic behavior and hazards. In May 1924, the century-long lava lake within Halemaʻumaʻu pit crater at the summit of Kīlauea Volcano drained and the floor of Halemaʻumaʻu collapsed, triggering ∼3 weeks of phreatic explosions due to the interaction of groundwater with hot rock. For the next three decades, eruptions at Kīlauea were sporadic (the longest hiatus was from 1934 to 1952), small in volume, and short (typically <1 month long). Here, we show that the Pb isotope ratios of Kīlauea lava groundmass and tephra glass samples erupted from 1912 to 1954 are anomalous and unusually variable. Many of the samples have elevated 207Pb/204Pb ratios (at a given 206Pb/204Pb), ranging up to ∼0.05 higher than is typical for Kīlauea lavas. The variations in 206Pb/204Pb for samples from 1912–1913 (∼0.055), 1917–1921 (∼0.120), 1923 (∼0.065), and 1952–1954 (∼0.037) are larger over short time periods (∼1–4 yr) than observed during the Puʻu ʻŌʻō rift eruption (only ∼0.031 from 1986 to 2012). These Pb isotopic signatures resulted from variable amounts of crustal contamination (most likely by Pb-rich hydrothermal sulfide minerals with high 207Pb/204Pb ratios) as the parental magmas transited the ∼110 Ma Pacific oceanic crust. This crustal contamination was not directly related to the shallow volcanic events of 1924. Instead, mantle-driven processes at Kīlauea during the previous century—a factor of ∼2 decrease in the degree of partial melting of an increasingly refractory source—led to a decline in the magma supply rate, a major disruption of the magmatic plumbing system, and, for at least a decade prior to 1924, crustal contamination at or below the base of the volcanic edifice (>10 km). The Pb isotopic heterogeneity of the samples on short length (hand specimen to lava flow) and time (∼1–4 yr) scales can be explained by inefficient mixing as small batches of contaminated magma were delivered to the remnants of Kīlauea’s summit magma storage reservoir. Our results confirm that the Pb isotope ratios of basalts from ocean-island volcanoes may be significantly modified by assimilation of materials from the underlying oceanic crust. In particular, the 207Pb/204Pb ratio may be a sensitive tracer of such crustal contamination at Hawaiian shield volcanoes. Mauna Loa lavas display a factor of ∼5 more scatter towards higher 207Pb/204Pb at a given 206Pb/204Pb ratio than most Kīlauea lavas (excluding the samples from 1912 to 1954). This might be caused by more pervasive crustal contamination at Mauna Loa due to its lower magma supply rate over the last ∼4 kyr.

Evidence for frequent, large tsunamis spanning locked and creeping parts of the Aleutian megathrust

Released May 27, 2019 15:00 EST

2019, Geological Society of America Bulletin (131) 707-729

Robert C. Witter, Richard W. Briggs, Simon E. Engelhart, Guy R. Gelfenbaum, Richard D Koehler, Alan R. Nelson, Seanpaul La Selle, Reide Corbett, Kristi Wallace

At the eastern end of the 1957 Andreanof Islands magnitude-8.6 earthquake rupture, Driftwood Bay (Umnak Island) and Stardust Bay (Sedanka Island) lie along presently locked and creeping parts of the Aleutian megathrust, respectively, based on satellite geodesy onshore. Both bays, located 200-km apart, face the Aleutian trench and harbor coastal evidence for tsunami inundation in 1957. Here we describe the evidence at Driftwood Bay, including eight sheets of landward-fining, normally-graded marine sand that extend up to 375-m inland and 23 m above mean tide level. Drift logs that corroborate historical accounts of 1957 tsunami runup on Umnak Island’s Pacific coast overlie the youngest sand sheet, which 137Cs activity shows was deposited in the decade before 1963. The older sand sheets probably record tsunamis prior to 1957 because an emergent coastal terrace lacks evidence for storm-wave erosion and overwash since ~2 ka. Comparisons of the Driftwood Bay and Stardust Bay tsunami histories suggest that at least twice in the past 1700 years inundation occurred at one site but not the other. In contrast, Bayesian age-depth modeling suggests that the two bays may record five tsunamis like the 1957 tsunami, generated by earthquake ruptures that spanned the presently locked and creeping parts of the Aleutian megathrust. However, serial tsunamis occurring within days to centuries cannot be precluded. Our findings imply 164–257-year recurrence intervals for large eastern Aleutian tsunamis and challenge the notion that creeping parts of the megathrust inferred from geodesy onshore pose lower earthquake and tsunami hazards than locked areas.

Ross Ice Shelf response to climate driven by the tectonic imprint on seafloor bathymetry

Released May 27, 2019 14:23 EST

2019, Nature Geoscience (12) 441-449

K J Tinto, L Padman, C S Siddoway, M.R. Springer, H.A. Fricker, I. Das, F. Caratori Tontini, D.F. Porter, N.P. Frearson, S. J. Howard, M.R. Siegfried, C. Mosbeux, M.K. Becker, C. Bertinato, A. Boghosian, N. Brady, Bethany L. Burton, W. Chu, S.I. Cordero, T. Dhakal, L. Dong, C.D. Gustafson, S. Keeshin, C. Locke, A. Lockett, G. O'Brien, J.J. Spergel, S.E. Starke, M. Tankersley, M. Wearing, R.E. Bell

Ocean melting has thinned Antarctica's ice shelves at an increasing rate over the past two decades, leading to loss of grounded ice. The Ross Ice Shelf is currently close to steady state but geological records indicate that it can disintegrate rapidly, which would accelerate grounded ice loss from catchments equivalent to 11.6 m of global sea level rise. Here, we use data from the ROSETTA-Ice airborne survey and new ocean simulations, to identify the principal threats to Ross Ice Shelf stability. We locate the tectonic boundary between East and West Antarctica from magnetic anomalies and use gravity data to generate a new high-resolution map of sub-ice-shelf bathymetry. The tectonic imprint on bathymetry constrains sub-ice-shelf ocean circulation, protecting the ice shelf grounding line from moderate changes in global ocean heat content. In contrast, local, seasonal production of warm upper-ocean water near the ice front drives rapid ice shelf melting east of Ross Island, where thinning would lead to faster grounded ice loss from both East and West Antarctic ice sheets. We confirm high modelled melt rates in this region using ROSETTA-Ice radar data. Our findings highlight the significance of both the tectonic framework and local ocean-atmosphere exchange processes near the ice front in determining the future of the Antarctic Ice Sheet.

Development and characterization of polymorphic microsatellite markers in Northern Fulmar, Fulmarus glacialis (Procellariformes), and cross-species amplification in eight other seabirds

Released May 27, 2019 10:07 EST

2019, Genes and Genomics

Megan C. Gravley, George K. Sage, Andrew M. Ramey, Scott A. Hatch, Verena A. Gill, Jolene R. Rearick, Aevar Petersen, Sandra L. Talbot


In the North Pacific, northern fulmar (Fulmarus glacialis) forms extensive colonies in few locales, which may lead to limited gene flow and locale-specific population threats. In the Atlantic, there are thousands of colonies of varying sizes and in Europe the species is considered threatened. Prior screens and classical microsatellite development in fulmar failed to provide a suite of markers adequate for population genetics studies.


The objective of this study was to isolate a suite of polymorphic microsatellite loci with sufficient variability to quantify levels of gene flow, population affinity, and identify familial relationships in fulmar. We also performed a cross-species screening of these markers in eight other species.


We used shotgun sequencing to isolate 26 novel microsatellite markers in fulmar to screen for variability using individuals from two distinct regions: the Pacific (Chagulak Island, Alaska) and the Atlantic (Hafnarey Island, Iceland).


Polymorphism was present in 24 loci in Chagulak and 23 in Hafnarey, while one locus failed to amplify in either colony. Polymorphic loci exhibited moderate levels of genetic diversity and this suite of loci uncovered genetic structuring between the regions. Among the other species screened, polymorphism was present in one to seven loci.


The loci yielded sufficient variability for use in population studies and estimation of familial relationships; as few as five loci provide resolution to determine individual identity. These markers will allow further insight into the global population dynamics and phylogeography of fulmars. We also demonstrated some markers are transferable to other species.

Conservation research across scales in a national program: How to be relevant to local management yet general at the same time

Released May 25, 2019 15:30 EST

2019, Biological Conservation (236) 100-106

Michael J. Adams, Erin L. Muths

Successfully addressing complex conservation problems requires attention to pattern and process at multiple spatial scales. This is challenging from a logistical and organizational perspective. In response to indications of worldwide declines in amphibian populations, the Amphibian Research and Monitoring Initiative (ARMI) of the United States Geological Survey was established in 2000. This national program is unique in its structure, organization, and success in integrating information at multiple scales. ARMI works under the principle that a good study design is tailored to specific questions, but stipulates the use of methods that result in unbiased parameter estimates (e.g., occupancy). This allows studies to be designed to address local questions but also to produce data that can easily be scaled up to accomplish the objectives of a broad-scale monitoring program. Here we describe how the implementation of the Amphibian Research and Monitoring Initiative results in research that is applicable across scales – global, in contributing to the understanding of amphibian decline phenomena; continental, in synthesizing local data to understand large-scale drivers; regional, by characterizing threats and assessing status of species at the range scale; and local, by working with National Park, Wildlife Refuge, and other Federal and State land managers to identify research needs and serve conservation-relevant research results to inform management decisions.

Vertical coseismic offsets from differential high-resolution stereogrammetric DSMs: The 2013 Baluchistan, Pakistan earthquake

Released May 25, 2019 09:50 EST

2019, Journal of Geophysical Research B: Solid Earth

William D. Barnhart, Ryan D. Gold, Hannah N. Shea, Katherine E. Peterson, Richard W. Briggs, David J. Harbor

The recent proliferation of high-resolution (< 3-m spatial resolution) digital topography datasets opens a spectrum of geodetic applications in differential topography, including the quantification of coseismic vertical displacement fields. Most investigations of coseismic vertical displacements to date rely, in part, on pre- or post-event lidar surveys that are intractable or non-existent in many locales. Stereogrammetric digital surface models (DSMs) derived from high-resolution satellite optical imagery provide a new avenue for the retrieval of spatially-dense vertical coseismic displacements on a global scale. In this study, we generated 2-m resolution pre- and post-seismic DSMs from satellite optical imagery spanning the 2013 Mw7.7 Baluchistan strike-slip earthquake that occurred on the Hoshab fault in southern Pakistan. We applied the Iterative Closest Point algorithm to the DSMs to quantify the coseismic vertical displacement field at a spatial resolution of 10-30 m and to generate 3D coseismic strain tensors. We found that across-fault vertical offsets alternated between uplift and subsidence and varied between ~1-3 m in a non-systematic manner along the Hoshab fault. We show that the pre-existing topography and near-fault geomorphology are variably consistent and inconsistent with the displacement kinematics of the 2013 earthquake, and we argue that these relationships highlight varied slip sense history along the Hoshab fault. Notably, topography along the southern extents of the Hoshab fault requires different surface displacement kinematics than occurred in the 2013 earthquake, suggesting that the Hoshab fault accommodates varying senses of slip (bimodal slip) through time.

Global phylodynamic analysis of avian paramyxovirus-1 provides evidence of inter-host transmission and intercontinental spatial diffusion

Released May 24, 2019 11:02 EST

2019, BMC Evolutionary Biology

Joseph T. Hicks, Kiril M. Dimitrov, Claudio L. Afonso, Andrew M. Ramey, Justin Bahl


Avian avulavirus (commonly known as avian paramyxovirus-1 or APMV-1) can cause disease of varying severity in both domestic and wild birds. Understanding how viruses move among hosts and geography would be useful for informing prevention and control efforts. A Bayesian statistical framework was employed to estimate the evolutionary history of 1602 complete fusion gene APMV-1 sequences collected from 1970 to 2016 in order to infer viral transmission between avian host orders and diffusion among geographic regions. Ancestral states were estimated with a non-reversible continuous-time Markov chain model, allowing transition rates between discrete states to be calculated. The evolutionary analyses were stratified by APMV-1 classes I (n = 198) and II (n = 1404), and only those sequences collected between 2006 and 2016 were allowed to contribute host and location information to the viral migration networks.


While the current data was unable to assess impact of host domestication status on APMV-1 diffusion, these analyses supported the sharing of APMV-1 among divergent host taxa. The highest supported transition rate for both classes existed from domestic chickens to Anseriformes (class I:6.18 transitions/year, 95% highest posterior density (HPD) 0.31–20.02, Bayes factor (BF) = 367.2; class II:2.88 transitions/year, 95%HPD 1.9–4.06, BF = 34,582.9). Further, among class II viruses, domestic chickens also acted as a source for Columbiformes (BF = 34,582.9), other Galliformes (BF = 34,582.9), and Psittaciformes (BF = 34,582.9). Columbiformes was also a highly supported source to Anseriformes (BF = 322.0) and domestic chickens (BF = 402.6). Additionally, our results provide support for the diffusion of viruses among continents and regions, but no interhemispheric viral exchange between 2006 and 2016. Among class II viruses, the highest transition rates were estimated from South Asia to the Middle East (1.21 transitions/year; 95%HPD 0.36–2.45; BF = 67,107.8), from Europe to East Asia (1.17 transitions/year; 95%HPD 0.12–2.61; BF = 436.2) and from Europe to Africa (1.06 transitions/year, 95%HPD 0.07–2.51; BF = 169.3).


While migration appears to occur infrequently, geographic movement may be important in determining viral diversification and population structure. In contrast, inter-order transmission of APMV-1 may occur readily, but most events are transient with few lineages persisting in novel hosts.

Toward explaining nitrogen and phosphorus trends in Chesapeake Bay tributaries, 1992-2012

Released May 24, 2019 10:50 EST

2019, Journal of the American Water Resources Association 1-20

Scott Ator, Ana Garcia, Gregory Schwarz, Joel Blomquist, Andrew Sekellick

Understanding trends in stream chemistry is critical to watershed management, and often complicated by multiple contaminant sources and landscape conditions changing over varying time scales. We adapted spatially-referenced regression (SPARROW) to infer causes of recent nutrient trends in Chesapeake Bay tributaries by relating observed fluxes during 1992, 2002, and 2012 to contemporary inputs and watershed conditions. The annual flow-normalized nitrogen flux to the bay from its watershed declined by 14 percent to 127,000 Mg (metric tons) between 1992 and 2012, due primarily (more than 80 percent of the decline) to reduced point sources. The remainder of the decline was due to reduced atmospheric deposition (13 percent) and urban non-point sources. Agricultural inputs, which contribute most nitrogen to the bay, changed little, although trends in the average nitrogen yield (flux per unit area) from cropland and pasture to streams in some settings suggest possible effects of evolving nutrient applications or other land management practices. Point sources of phosphorus to local streams declined by half between 1992 and 2012, while non-point inputs were relatively unchanged. Annual phosphorus delivery to the bay increased by 9 percent to 9,570 Mg between 1992 and 2012, however, due mainly to reduced retention in the Susquehanna River at Conowingo Reservoir.

Drilling, construction, water chemistry, water levels, and regional potentiometric surface of the upper carbonate-rock aquifer in Clark County, Nevada, 2009–2015

Released May 23, 2019 15:22 EST

2019, Scientific Investigations Map 3434

Jon W. Wilson

The U.S. Geological Survey (USGS) and the Bureau of Land Management (BLM) initiated a cooperative study through the Southern Nevada Public Land Management Act (Bureau of Land Management, 1998) to install six wells in the carbonate-rock and basin-fill aquifers of Clark County, Nevada, in areas of sparse groundwater data. This map uses water levels from these new wells, water levels from existing wells, and altitudes of spring discharge points to update a regional potentiometric map of the carbonate-rock aquifer and provide evidence to interpret the direction of regional groundwater flow. This potentiometric surface map is accompanied by drilling and borehole geophysical logs, well construction information, lithology, water chemistry, and water levels from the newly drilled wells.

A comparison of riparian vegetation sampling methods along a large, regulated river

Released May 23, 2019 15:18 EST

2019, River Research and Applications

Emily C. Palmquist, Sarah Sterner, Barbara Ralston

Monitoring riparian vegetation cover and species richness is an important component of assessing change and understanding ecosystem processes. Vegetation sampling methods determined to be the best option in other ecosystems (e.g., desert grasslands and arctic tundra) may not be the best option in multilayered, species rich, heterogeneous riparian vegetation. This study examines the strengths and weaknesses of two common vegetation sampling methods, line‐point intercept and ocular quadrat estimates. Permutational analysis of variance analyses indicate that cover estimates among observers did not differ significantly for either line‐point intercept or ocular quadrat estimates. Line‐point intercept cover estimates resulted in lower coefficient of variation among observers than ocular quadrat estimates, but the ocular quadrat estimates recorded significantly more species. Line‐point estimates of cover were generally larger than ocular quadrat estimates. Ocular quadrat estimates are appropriate when assessment of richness is important, in areas with heterogeneous geomorphology and hydrology where fine‐scale measurements are most useful, and in areas where continuous sampling transects are impracticable. Line‐point intercept estimates are useful when minimum variation among observers is necessary, continuous transects are logical and practicable for the sampling area, woody cover does not present a logistical complication, and species richness is not a priority.

San Francisco Bay triennial bird egg monitoring program for contaminants, California—2018

Released May 23, 2019 14:38 EST

2019, Data Series 1114

Joshua T. Ackerman, C. Alex Hartman, Mark P. Herzog, Matthew Toney

The Regional Monitoring Program for Water Quality in San Francisco Bay (RMP), administered by the San Francisco Estuary Institute, is a large-scale effort to monitor contaminant trends in water, sediment, fish, and birds throughout San Francisco Bay (San Francisco Estuary Institute, 2016). As part of the RMP and the U.S. Geological Survey (USGS) long-term Wildlife Contaminants Program, the USGS samples doublecrested cormorant (Phalacrocorax auritus) and Forster’s tern (Sterna forsteri) eggs throughout the San Francisco Bay approximately every 3 years to assess temporal trends in contaminant concentrations. This sampling has previously been carried out by USGS in 2009, 2012, and 2016. This document summarizes egg collections for 2018, as well as mercury concentrations in Forster’s tern eggs on an individual egg basis. These data are available in a USGS data release (Ackerman and others, 2019).

Dam effects on bedload transport on the upper Santa Ana River, California, and implications for native fish habitat

Released May 23, 2019 14:35 EST

2019, River Research and Applications 1-14

Scott A. Wright, J Toby Minear

Dams disrupt the flow of water and sediment and thus have the potential to affect the downstream geomorphic characteristics of a river. Though there are some well‐known and common geomorphic responses to dams, such as bed armouring, the response downstream from any particular dam is dependent on local conditions. Herein, we investigate the response of the upper Santa Ana River in southern California, USA, to the construction of a large dam at the transition from mountains to valley, using calculations of bedload transport capacity on the mainstem below the dam and for major tributaries. Approximate sediment budgets were constructed for downstream reaches to estimate deposition and erosion rates for sand, gravel, and cobble particle sizes. Our results indicate that the classical response of bed armouring and erosion is likely limited to a short reach immediately below the dam. Farther downstream, though transport capacity is reduced by flow regulation by the dam, the channel reaches are likely to remain depositional but with reduced deposition rates. Persistent deposition, as opposed to erosion, is the result of the replenishment of flow and sediment supply by large downstream tributaries. In addition, the calculations indicate that the composition of the bed is unlikely to change substantially in downstream reaches. A Monte Carlo approach was employed to estimate the uncertainty in the sediment budget predictions. The impacts of the dam on the geomorphic character of the river downstream could have implications for native fish that rely on coarse substrate that supports their food base.

Turbidity current observations in a large reservoir following a major wildfire

Released May 23, 2019 14:28 EST

2019, Journal of Hydrologic Engineering (145)

Scott A. Wright, Mathieu D. Marineau

Turbidity currents are generated when denser river water plunges and flows along the bottom of a lake, reservoir, or ocean. The plunging and downstream movement are driven by density differences due to temperature and/or suspended sediment, and currents have been observed to move slowly over long distances. This study presents observations of multiple turbidity currents in a large reservoir in California, United States, during runoff events following a major wildfire in the upstream watershed. Several aspects of the currents are documented and discussed, including the conditions leading to plunging, the vertical and longitudinal structure of turbidity within the currents, the velocity of the currents, and the development of a muddy lake upstream from an old submerged dam in the reservoir.

Climate adaptation Science Centers—Annual report for 2018

Released May 23, 2019 13:00 EST

2019, Open-File Report 2019-1041

Elda Varela Minder

2018 marked the 10-year anniversary of the establishment of the U.S. Geological Survey (USGS) National Climate Change and Wildlife Science Center! With the passage of the fiscal year 2018 budget on March 23, 2018, our program name was changed from the National Climate Change and Wildlife Science Center to the National Climate Adaptation Science Center (NCASC). The eight regional Department of the Interior (DOI) Climate Science Centers were renamed Climate Adaptation Science Centers (CASCs). The name changes more clearly align the national and regional centers and emphasize their focus on meeting natural resource adaptation needs. Although the program has a new name, our mission has not changed. We are still hard at work delivering science to help fish, wildlife, water, land, and people adapt to a changing climate.

During the past 10 years, the NCASC and the eight regional CASCs funded over 425 science projects and built a network of research partners, resource management stakeholders, interdisciplinary staff, fellows, and early career researchers. In celebration of our work and accomplishments over the last 10 years, the NCASC began a monthly web post series on “10 Things You May Not Know” about topics our science has focused on, including drought, glaciers, and wildfire.

Additionally, CASCs that had completed their initial hosting agreement with the USGS underwent a formal review and recompetition process. New hosting agreements were awarded to the Southwest and North Central CASCs in 2018. Read the 2018 annual report to learn more about the CASCs' great science, partnerships, capacity building, and more from 2018.

Atrazine induced transgenerational reproductive effects in medaka (Oryzias latipes)

Released May 22, 2019 16:27 EST

2019, Environmental Pollution (251) 639-650

Jacob A. Cleary, Donald E. Tillitt, Fredrick S. vom Saal, Diane Nicks, Rachel Claunch, Ramji K. Bhandari

Atrazine is presently one of the most abundantly used herbicides in the United States, and a common contaminant of natural water bodies and drinking waters in high-use areas. Dysregulation of reproductive processes has been demonstrated in atrazine exposed fish, including alteration of key endocrine pathways on hypothalamic-pituitary-gonadal (HPG) axis. However, the potential for atrazine-induced transgenerational inheritance of reproductive effects in fish has not been investigated. The present study examined the effects of early developmental atrazine exposure on transgenerational reproductive dysregulation in Japanese medaka (Oryzias latipes). F0 medaka were exposed to atrazine (ATZ, 5 or 50 μg/L), 17α-ethinylestradiol (EE2, 0.002 or 0.05 μg/L), or solvent control during the first twelve days of development with no subsequent exposure over three generations. This exposure overlapped with the critical developmental window for embryonic germ cell development, gonadogenesis, and sex determination. Exposed males and females of the F0 generation were bred to produce an F1 generation, and this was continued until the F2 generation. Sperm count and motility were not affected in F0 males; however, both parameters were significantly reduced in the males from F2 Low EE2 (0.002 μg/L), Low ATZ (5 μg/L), and High ATZ (50 μg/L) lineages. Fecundity was unaffected by atrazine or EE2 in F0 through F2 generations; however, fertilization rate was decreased in low atrazine and EE2 exposure lineages in the F2 generation. There were significant transgenerational differences in expression of the genes involved in steroidogenesis and DNA methylation. These results suggest that although early life exposure to atrazine did not cause significant phenotypes in the directly exposed F0 generation, subsequent generations of fish were at greater risk of reproductive dysfunction.

Mapping cropland extent of Southeast and Northeast Asia using multi-year time-series Landsat 30-m data using Random Forest classifier on Google Earth Engine

Released May 22, 2019 16:11 EST

2019, International Journal of Applied Earth Observation and Geoinformation (81) 110-124

Adam Oliphant, Prasad S. Thenkabail, Pardhasaradhi Teluguntla, Jun Xiong, Murali Krishna Gumma, Russell G. Congalton, Kamini Yadav

Cropland extent maps are useful components for assessing food security. Ideally, such products are a useful addition to countrywide agricultural statistics since they are not politically biased and can be used to calculate cropland area for any spatial unit from an individual farm to various administrative unites (e.g., state, county, district) within and across nations, which in turn can be used to estimate agricultural productivity as well as degree of disturbance on food security from natural disasters and political conflict. However, existing cropland extent maps over large areas (e.g., Country, region, continent, world) are derived from coarse resolution imagery (250 m to 1 km pixels) and have many limitations such as missing fragmented and\or small farms with mixed signatures from different crop types and\or farming practices that can be, confused with other land cover. As a result, the coarse resolution maps have limited useflness in areas where fields are small (<1 ha), such as in Southeast Asia. Furthermore, coarse resolution cropland maps have known uncertainties in both geo-precision of cropland location as well as accuracies of the product. To overcome these limitations, this research was conducted using multi-date, multi-year 30-m Landsat time-series data for 3 years chosen from 2013 to 2016 for all Southeast and Northeast Asian Countries (SNACs), which included 7 refined agro-ecological zones (RAEZ) and 12 countries (Indonesia, Thailand, Myanmar, Vietnam, Malaysia, Philippines, Cambodia, Japan, North Korea, Laos, South Korea, and Brunei). The 30-m (1 pixel = 0.09 ha) data from Landsat 8 Operational Land Imager (OLI) and Landsat 7 Enhanced Thematic Mapper (ETM+) were used in the study. Ten Landsat bands were used in the analysis (blue, green, red, NIR, SWIR1, SWIR2, Thermal, NDVI, NDWI, LSWI) along with additional layers of standard deviation of these 10 bands across 1 year, and global digital elevation model (GDEM)-derived slope and elevation bands. To reduce the impact of clouds, the Landsat imagery was time-composited over four time-periods (Period 1: January- April, Period 2: May-August, and Period 3: September-December) over 3-years. Period 4 was the standard deviation of all 10 bands taken over all images acquired during the 2015 calendar year. These four period composites, totaling 42 band data-cube, were generated for each of the 7 RAEZs. The reference training data (N = 7849) generated for the 7 RAEZ using sub-meter to 5-m very high spatial resolution imagery (VHRI) helped generate the knowledge-base to separate croplands from non-croplands. This knowledge-base was used to code and run a pixel-based random forest (RF) supervised machine learning algorithm on the Google Earth Engine (GEE) cloud computing environment to separate croplands from non-croplands. The resulting cropland extent products were evaluated using an independent reference validation dataset (N = 1750) in each of the 7 RAEZs as well as for the entire SNAC area. For the entire SNAC area, the overall accuracy was 88.1% with a producer’s accuracy of 81.6% (errors of omissions = 18.4%) and user’s accuracy of 76.7% (errors of commissions = 23.3%). For each of the 7 RAEZs overall accuracies varied from 83.2 to 96.4%. Cropland areas calculated for the 12 countries were compared with country areas reported by the United Nations Food and Agriculture Organization and other national cropland statistics resulting in an R2 value of 0.93. The cropland areas of provinces were compared with the province statistics that showed an R2 = 0.95 for South Korea and R2 = 0.94 for Thailand. The cropland products are made available on an interactive viewer at www.croplands.org and for download at National Aeronautics and Space Administration’s (NASA) Land Processes Distributed Active Archive Center (LP DAAC): https://lpdaac.usgs.gov/node/1281.

The importance of groundwater flow to the formation of modern thrombolitic microbialites

Released May 22, 2019 15:12 EST

2019, Geobiology

John Warden, Lee Coshell, Michael R. Rosen, Daniel O. Breecker, Katinka X. Ruthrof, Christopher R. Omelon

Modern microbialites are often located within groundwater discharge zones, yet the role of groundwater in microbialite accretion has yet to be resolved. To understand relationships between groundwater, microbialites, and associated microbial communities, we quantified and characterized groundwater flow and chemistry in active thrombolitic microbialites in Lake Clifton, Western Australia, and compared these observations to inactive thrombolites and lakebed sediments. Groundwater flows upward through an interconnected network of pores within the microstructure of active thrombolites, discharging directly from thrombolite heads into the lake. This upwelling groundwater is fresher than lake water and is hypothesized to support microbial mat growth by reducing salinity and providing limiting nutrients in an osmotically stressful and oligotrophic habitat. This is in contrast to inactive thrombolites that show no evidence of microbial mat colonization and are infiltrated by hypersaline lake water. Groundwater discharge through active thrombolites contrasts with the surrounding lakebed, where hypersaline lake water flows downward through sandy sediments at very low rates. Based on an appreciation for the role of microorganisms in thrombolite accretion, our findings suggest conditions favorable to thrombolite formation still exist in certain locations of Lake Clifton despite increasing lake water salinity. This study is the first to characterize groundwater flow rates, paths, and chemistry within a microbialite‐forming environment and provides new insight into how groundwater can support microbial mats believed to contribute to microbialite formation in modern and ancient environments.

Groundwater quality in the Delaware, Genesee, and St. Lawrence River Basins, New York, 2015

Released May 22, 2019 11:30 EST

2019, Open-File Report 2019-1005

Tia-Marie Scott, Elizabeth A. Nystrom, James E. Reddy

The U.S. Geological Survey, in cooperation with the New York State Department of Environmental Conservation, collected groundwater samples from 5 production wells and 5 domestic wells in the Delaware River Basin, 8 production wells and 7 domestic wells in the Genesee River Basin, and 1 municipal well, 7 production wells, and 13 domestic wells in the St. Lawrence River Basin in New York. All samples were collected from May through November 2015 in an effort to characterize groundwater quality in these basins. The samples were collected and processed by using standard U.S. Geological Survey procedures and were analyzed for 148 physiochemical properties and constituents, including dissolved gases, major ions, nutrients, trace elements, pesticides, volatile organic compounds, radionuclides, and indicator bacteria.

The Delaware River Basin study area covers 2,360 square miles (mi2) in southeastern New York. Of the 10 wells sampled in the Delaware River Basin, 3 are completed in sand and gravel, and 7 are completed in bedrock. Groundwater in the Delaware River Basin was generally of good quality, although properties and concentrations of some constituents—pH, iron, manganese, aluminum, radon-222, and total coliform bacteria—sometimes equaled or exceeded primary, secondary, or proposed drinking-water standards. The constituent most frequently detected in concentrations exceeding drinking-water standards (10 of 10 samples) was radon-222.

The Genesee River Basin study area includes the entire 2,439 mi2 of the basin in western New York. Of the 15 wells sampled in the Genesee River Basin, 6 are completed in sand and gravel, and 9 are completed in bedrock. Groundwater in the Genesee River Basin was generally of good quality, although properties and concentrations of some constituents—chloride, sodium, dissolved solids, iron, manganese, aluminum, arsenic, radon-222, methane, total coliform bacteria, fecal coliform bacteria, and Escherichia coli bacteria—sometimes equaled or exceeded primary, secondary, or proposed drinking-water standards. The constituent most frequently detected in concentrations exceeding drinking-water standards (12 of 15 samples) was radon-222.

The St. Lawrence River Basin study area includes the entire 5,650 mi2 of the basin in northeastern New York. Of the 21 wells sampled in the St. Lawrence River Basin, 7 are completed in sand and gravel, and 14 are completed in bedrock. Groundwater in the St. Lawrence River Basin was generally of good quality, although properties and concentrations of some constituents—pH, chloride, sodium, dissolved solids, iron, manganese, sulfate, nitrate, radon-222, total coliform bacteria, fecal coliform bacteria, and Escherichia coli bacteria—sometimes equaled or exceeded primary, secondary, or proposed drinking-water standards. The constituent most frequently detected in concentrations exceeding drinking-water standards (14 of 21 samples) was radon-222.

Sea-cliff bedstraw (Galium buxifolium) patterns and trends, 2005–14, on Santa Cruz and San Miguel Islands, Channel Islands National Park, California

Released May 22, 2019 08:38 EST

2019, Open-File Report 2019-1054

Kathryn McEachern, Katherine A. Chess, Karen Flagg, Kenneth G. Niessen

Sea-cliff bedstraw (Galium buxifolium [Rubiaceae]) is a delicate dioecious subshrub endemic to Santa Cruz and San Miguel Islands, in the northern California Channel Islands. It was listed as endangered in 1997 under the Federal Endangered Species Act, threatened by soil loss, habitat alteration, and herbivory from more than a century of ranching land use. At the time of listing, there were eight populations known from Santa Cruz Island and two from San Miguel Island, restricted to shaded, northfacing volcanic ocean bluffs. The recovery plan included criteria to be considered for delisting such as stabilizing or increasing populations on both islands and recovery actions such as searching for more populations, seed banking, researching seed germination and life history, and reversing factors causing decline.

We began studying sea-cliff bedstraw on Santa Cruz Island in the early 2000s to better understand factors related to decline. We surveyed historic populations and searched for new occurrences 2004–06, researched population size-class structure and floral biology 2005–06 at three sites, and tracked demography 2005–14 while treating the invasive periwinkle (Vinca major) with herbicide at a fourth site. We collected seeds for germination studies and long-term seed banking from all four study sites.

The historically known Santa Cruz Island sites were still extant on the sea-cliffs, and we located 14 occurrences not documented at the time of listing. Sea-cliff bedstraw floral morphology appears evenly balanced between mainly pistillate and staminate plants at the study sites, with other floral types present as well, in the populations we sampled. Seed germination trials showed about a 40 percent germination rate from fresh imbibed seeds. Life-history stage structure 2005–06 varied from purely reproductive plants at one site to nearly equal representation of vegetative and reproductive plants at a second site, with seedlings also present at the remaining two sites.

Demographic study of tagged plants at the long-term study plot 2005–14 showed an episodic pattern of high recruitment with low mortality once plants became established beyond the first summer dormant season. A flush of seedlings was seen after periwinkle reduction, indicating that the periwinkle may have been repressing seedling establishment. About 93 percent of the already-established plants tagged in 2005 and 2006 were still present 10 years later in 2014. Findings indicate that sea-cliff bedstraw individuals are long-lived and once established have good survival rates. Taken together, these results imply that population growth is driven more by germination and recruitment into the mature population than by mortality of established plants, at least since feral animal eradication from Santa Cruz Island. Therefore, conservation actions might be best focused on nurturing safe sites for seed germination and seedling survival.

Petrographic, geochemical, and geochronologic data for cenozoic volcanic rocks of the Tonopah, Divide, and Goldfield Mining Districts, Nevada

Released May 21, 2019 12:10 EST

2019, Data Series 1099

Edward A. du Bray, David A. John, Peter G. Vikre, Joseph P. Colgan, Michael A. Cosca, Leah E. Morgan, Robert J. Fleck, Wayne R. Premo, Christopher S. Holm-Denoma

The purpose of this report is to summarize geochemical, petrographic, and geochronologic data for samples, principally those of unmineralized Tertiary volcanic rocks, from the Tonopah, Divide, and Goldfield mining districts of west-central Nevada (fig. 1). Much of the data presented here for the Tonopah and Divide districts are for samples collected by Bonham and Garside (1979) during geologic mapping in and around those districts, whereas much of that for samples from the Goldfield district were obtained by Ashley (1974; 1979; 1990a). Additional data were derived from samples collected between 2012–2015, as part of the Mineral Resources Program funded project titled: “Magmatic-tectonic history and component sources of major precious metal deposits in the southern Walker Lane”. A small amount of additional geochemical data for samples from each of the districts were compiled from other sources. Individual sample collectors are identified by appropriate entries in the “Collector” field (appendix 1) and published sources of geochemical data are defined by entries in the “Chem_Src” data field (appendix 1).

Radiometric ages of volcanic rocks on the fort rock dome and in the aquarius mountains, Yavapai and Mohave Counties, Arizona

Released May 21, 2019 10:18 EST

2019, Open-File Report 2019-1038

Gary S. Fuis, Andrew T. Calvert, Katie Sullivan

The Fort Rock dome, in Yavapai County, Ariz., is a roughly circular geologic structure in plan view, 2.5 km in diameter, that is similar in many ways to an impact crater; however, it is a structural dome caused by a potassic mafic intrusion at depth, and the crater-like depression in its center is erosional in origin. The Aquarius Mountains, west of the Fort Rock dome, in Mohave County, contain a felsic volcanic center that erupted tuffs, non-welded ash-flow tuffs, and lahars following dome emplacement.

This report discusses the radiometric ages of samples of rock units from both the Fort Rock dome and the Aquarius Mountains eruptive center. The ages for all samples span a short interval of time from 22.3 to 21.7 m.y. (earliest Miocene). The individual sample ages are consistent with the stratigraphic order of the rock units in the area, and the short age span is consistent with the absence of any significant unconformities in the section.

Monitoring volcanic deformation

Released May 21, 2019 09:00 EST

2019, Book chapter, Reference Module in Earth Systems and Environmental Sciences

Maurizio Battaglia, Jorge Alpala, Rosa Alpala, Mario Angarita, Dario Arcos, Leonardo Eullides, Pablo Euillades, Cyrill Mueller, Lourdes Narvaez

Whereas research in volcano geodesy seeks to push the boundaries of our knowledge of the physics of volcanoes, monitoring looks at changes in volcano behavior to predict when a volcanic crisis might develop. To be effective, geodetic monitoring must be done before, during, and after eruptions and must be integrated with other monitoring techniques. It requires the type of long-term commitment of time and resources that academic and industry scientists generally cannot make. A few, well-placed geodetic monitoring stations can make a huge difference to a country's ability to alert its people to an imminent volcanic eruption.

Monitoring strategies vary greatly depending on several factors such as the activity of the individual volcano, access, and available personnel and funding. Rapid advances in technology allow for more precise geodetic monitoring today than was imaginable when many of the existing volcano observatories were established. Today, deformation measurements at active volcanoes are usually made with continuous Global Positioning System (CGPS) stations, supplemented by Interferometric Synthetic Aperture Radar (InSAR) images. Neither method requires a continuous presence of personnel in the field, except for the installation and maintenance of the GPS stations; however subsequent data analysis can be highly complex.

Optimizing an inner-continental shelf geologic framework investigation through data repurposing and machine learning

Released May 21, 2019 08:48 EST

2019, Geosciences (9)

Elizabeth A. Pendleton, Laura L. Brothers, Ed Sweeney

The U.S. Geological Survey (USGS) and the National Oceanic Atmospheric Administration (NOAA) have collected approximately 5,400 km2 of geophysical and hydrographic data on the Atlantic continental shelf between Delaware and Virginia over the past decade and a half. Although originally acquired for different objectives, the comprehensive coverage and variety of data (bathymetry, backscatter, imagery and physical samples) presents an opportunity to merge collections and create high-resolution, broad-scale geologic maps of the seafloor. This compilation of data repurposes hydrographic data, expands the area of geologic investigation, highlights the versatility of mapping data, and creates new geologic products that would not have been independently possible. The data are classified using a variety of machine learning algorithms, including unsupervised and supervised methods. Four unique classes were targeted for classification, and source data include bathymetry, backscatter, slope, curvature, and shaded-relief. A random forest classifier used on all five source data layers was found to be the most accurate method for these data. Geomorphologic and sediment texture maps are derived from the classified acoustic data using over 200 groundtruth samples. The geologic data products can be used to identify sediment sources, inform resource management, link seafloor environments to sediment texture, improve our understanding of seafloor structure and sediment pathways, and demonstrate how ocean mapping resources can be useful beyond their original intent to maximize the footprint and scientific impact of a study.

The pathogenesis of H7 highly pathogenic avian influenza viruses in Lesser Scaup (Aythya affinis)

Released May 21, 2019 08:42 EST

2019, Avian Diseases (63) 230-234

Christopher B. Stephens, Diann Prosser, Mary J. Pantin-Jackwood, Alicia Berlin, Erica Spackman

Waterfowl are the natural hosts of avian influenza virus (AIV), and through migration spread the virus worldwide. Most AIVs carried by wild waterfowl are low pathogenic strains; however, Goose/Guangdong/1996 lineage clade H5 highly pathogenic (HP) AIV now appears to be endemic in wild birds in much of the Eastern Hemisphere. Most research efforts studying AIV pathogenicity in waterfowl thus far have been directed toward dabbling ducks. In order to better understand the role of diving ducks in AIV ecology, we previously characterized the pathogenesis of clade H5 HPAIV in lesser scaup (Aythya affinis). In an effort to further elucidate AIV infection in diving ducks, the relative susceptibility and pathogenesis of two North American lineage H7 HPAIV isolates from the most recent outbreaks in the United States was investigated. Lesser scaup were inoculated with either A/turkey/IN/1403-1/2016 H7N8 or A/chicken/TN/17-007147-2/2017 H7N9 HPAIV by the intranasal route. The approximate 50% bird infectious dose (BID50) of the H7N8 isolate was determined to be 103 50% egg infectious doses (EID50), and the BID50 of the H7N9 isolate was determined to be <102 EID50, indicating some variation in adaptation between the two isolates. No mortality or clinical disease was observed in either group except for elevated body temperatures at 2 and 4 days postinoculation (DPI). Virus shedding was detected up to 14 DPI from both groups, and there was a trend for shedding to have a longer duration and at higher titer levels from the cloacal route. These results demonstrate that lesser scaup are susceptible to both H7 lineages of HPAIV, and similar to dabbling duck species, they shed virus for long periods relative to gallinaceous birds and don't present with clinical disease.

Spatially explicit modelling of floodplain forest succession: Interactions among flood inundation, forest successional processes, and other disturbances in the Upper Mississippi River floodplain, USA

Released May 21, 2019 08:35 EST

2019, Ecological Modelling (405) 15-32

Nathan R. De Jager, Molly Van Appledorn, Timothy J. Fox, Jason J. Rohweder, Lyle J. Guyon, Andrew R. Meier, Robert J. Cosgriff, Benjamin J. Vandermyde

Simulation models are often used to identify hydrologic regimes suitable for different riparian or floodplain tree species. However, most existing models pay little attention to forest successional processes or other disturbances that may interact with the hydrologic regime of river systems to alter forest dynamics in space and time. In this study, we introduce a flood disturbance module to the LANDIS-II forest succession modelling framework to enable investigations into how inundation interacts with other disturbances and successional processes to alter floodplain forest cover and community dynamics. We illustrate the functionality of the model using a case study with multiple scenarios in the Upper Mississippi River floodplain, USA. We found that model predictions of total forest cover and the abundance of specific forest community types were generally related to uncertainty in the susceptibility of different species and age classes to inundation. By simulation year 100, increases or decreases in total forest cover and forest type distributions were roughly proportional to the initial differences in the susceptibility of species and age classes to inundation. The largest decrease in total forest cover was associated with a scenario that included disturbance by the emerald ash borer (Agrilus planipennis) and when using susceptibility parameters corresponding to the weakest flood tolerance. In contrast, changes in the composition of aboveground biomass were not sensitive to differences in susceptibility, and generally showed shifts toward later successional species with higher shade tolerance and longer lifespans for all scenarios. Our findings suggest that flood inundation interacts with other disturbances (e.g., insect outbreaks) and forest successional processes to alter forest abundance, distribution, and species composition in this system. Our modelling framework should allow for future studies that examine such interactions in other systems, and in the context of alternative hydrologic scenarios and other disturbance regimes.

Knowing your limits: Estimating range boundaries and co-occurrence zones for two competing plethodontid salamanders

Released May 21, 2019 08:29 EST

2019, Ecosphere (10) 1-19

S. M. Amburgey, D. A. W. Miller, Adrianne B, Brand, Andrea M. Dietrich, Evan H. Campbell Grant

Understanding threats to species persistence requires knowledge of where species currently occur. We explore methods for estimating two important facets of species distributions, namely where the range limit occurs and how species interactions structure distributions. Accurate understanding of range limits is crucial for predicting range dynamics and shifts in response to interspecific interactions and climate change. Additionally, species interactions are increasingly recognized as an important but not well‐understood predictor of range shifts. Our objective was to predict range limits and contact zones for two plethodontid salamanders, the highly range‐restricted Shenandoah salamander (Plethodon shenandoah) and the wide‐ranging red‐backed salamander (Plethodon cinereus). Using detection/non‐detection data, we assess four methodological decisions when estimating species’ distributions: (1) accounting for imperfect detection, (2) covariates to predict species occurrences, (3) accounting for species interactions, and (4) the inclusion of spatial autocorrelation. We found that Shenandoah salamander and red‐backed salamander co‐occurrence would have been underestimated and the range edge misidentified had we not accounted for incomplete detection. Covariates related to habitat were not sufficient to explain species’ range boundaries. Models that included spatial autocorrelation (i.e., a conditional autoregressive random effect) performed better than models that included just species interactions (i.e., detection and occurrence were conditional on the other species being present) and models that included both spatial autocorrelation and species interactions. Further, we found that the breadth of primary contact zones was typically 60–170 m, which is greater on average than previous estimates. In addition, we frequently observed secondary, disjunct contact zones along the range boundary. Understanding the extent to which species co‐occur and how the range boundaries are shaped is crucial to conservation efforts. Our work indicates that accounting for detection is crucial for accurately characterizing range edges and that spatial models may be especially effective in modeling distributions at the boundary.

Assessing water quality from highway runoff at selected sites in North Carolina with the Stochastic Empirical Loading and Dilution Model (SELDM)

Released May 20, 2019 17:00 EST

2019, Scientific Investigations Report 2019-5031

J. Curtis Weaver, Gregory E. Granato, Sharon A. Fitzgerald

In 2015, the U.S. Geological Survey (USGS) entered into a cooperative agreement with the North Carolina Department of Transportation (NCDOT) to develop a North Carolina-enhanced variation of the national Stochastic Empirical Loading and Dilution Model (SELDM) with available North Carolina-specific streamflow and water-quality data and to demonstrate use of the model by documenting selected simulation scenarios. The USGS developed the national SELDM in cooperation with the Federal Highway Administration to provide the tools and techniques necessary for performing stormwater-quality simulations. SELDM uses a stochastic mass-balance approach to estimate combinations of flows, concentrations, and loads of stormwater constituents from the site of interest (often a highway catchment; nonhighway areas, such as a large impervious area at a shopping center complex, also can be used) and the basin upstream from the stormwater outfall to assess the risk for adverse effects of runoff. SELDM also can be used to simulate the effectiveness of volume reduction, hydrograph extension, and water-quality concentration reductions by stormwater best management practices (BMPs), which are designed to help mitigate the effects of runoff on receiving water bodies.

Some of the statistical inputs needed for the North Carolina-enhanced SELDM were either calculated or augmented using local or regional data from North Carolina. Streamflow statistics used by SELDM were determined for 266 streamgages across North Carolina on the basis of data available through the 2015 water year. Recession ratio statistics used for triangular hydrographs were also developed for 30 streamgages across the State. The NCDOT identified previous research reports on highway-runoff and BMP studies in North Carolina for review of potential data addition to the national FHWA Highway-Runoff Database (HRDB). Following USGS review of these data, a total of 25,087 event mean concentration values and 1,140 storm events for 39 highway-runoff sites and 195 analytes were uploaded to the national HRDB from six North Carolina highway-runoff research reports and a recent USGS bridge deck runoff study. Using data for 27 streamgages in North Carolina, a total of 57 water-quality transport curves were developed for seven constituents for use in simulating water-quality conditions in the upstream basin. Performance data for three BMPs (bioretention, grass strip or swale, and wetland channel) from NCDOT research data were incorporated into the North Carolina-enhanced SELDM for volume-reduction statistics, including the effectiveness of treating four water-quality constituents (total suspended solids, total nitrogen, total phosphorus, nitrate plus nitrite) and turbidity.

Simulations using the North Carolina-enhanced SELDM are presented for two hypothetical upstream basins in the Piedmont ecoregion and one hypothetical highway site to demonstrate how simulations can be used to provide risk-based information about potential effects of stormwater runoff on downstream water quality and the potential for mitigating those risks by using BMPs. The first group of simulations explores the stochastic variability in dilution factors (the ratio of the highway runoff to the total downstream stormflow) for a hypothetical Piedmont rural creek having drainage areas ranging from 1 to 100 square miles. The second group of simulations examines dilution factors based on variations in precipitation, streamflow, and recession ratios for two hypothetical Piedmont upstream basins (rural and urban) where the drainage area was held constant at 25 square miles. These simulations indicate the sensitivity of results to variations in each of the three variables. The third group of simulations examines the effects of varied concentrations in the upstream basin on water-quality conditions downstream from the highway crossing. Variations in upstream water-quality conditions for three constituents (suspended sediment concentration, total nitrogen, and total phosphorus) are based on water-quality transport curves selected from among the 57 curves developed as part of this study to represent low-, medium-, and high-concentration statistics. Simulations completed for this third group also examine the potential effects of grass swale and bioretention BMP treatment on total nitrogen and total phosphorus concentrations in highway runoff. The BMP performance data from the NCDOT research reports were applied in this group of simulations.

The stochastic mass-balance approach used in SELDM analyses and simulations provides a strong tool for engineers and water-resource managers to use in exploring a wide range of possible hydrologic and water-quality inputs and their effects on downstream water quality. The results of this study can not only aid engineers and managers in planning for potential adverse effects of runoff at site-specific locations, they can also help the USGS and other Federal and State agencies with oversight responsibilities in stormwater-quality issues to continue gathering data on potential water-quality effects in receiving streams.

Context matters: Using reinforcement learning to develop human-readable, state-dependent outbreak response policies

Released May 20, 2019 10:26 EST

2019, Philosophical Transactions of the Royal Society B: Biological Sciences (374) 1-9

William J M Probert, Sandya Lakkur, Christopher J Fonnesbeck, Katriona Shea, Michael C. Runge, Michael J. Tildesley, Matthew J Ferrari

The number of all possible epidemics of a given infectious disease that could occur on a given landscape is large for systems of real-world complexity. Furthermore, there is no guarantee that the control actions that are optimal, on average, over all possible epidemics are also best for each possible epidemic. Reinforcement learning (RL) has been used to develop machine-readable context-dependent solutions for complex problems with many possible realisations ranging from video-games to the game of Go. RL could be a valuable tool to generate context-dependent policies for outbreak response, though translating the resulting policies into simple rules that can be read and interpreted by human decision-makers remains a challenge. Here we illustrate the application of RL to the development of context-dependent outbreak response policies to minimise outbreaks of foot-and-mouth disease. We show that control based on the resulting context-dependent policies, which adapt interventions to the specific outbreak, result in smaller outbreaks than static policies. We further illustrate two approaches for translating the complex machine-readable policies into simple heuristics that can be evaluated by human decision-makers.