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Publications recently added to the Pubs Warehouse

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Monitoring breeding and survival of ring-necked pheasant (Phasianus colchicus) in the Sacramento Valley, Sacramento-San Joaquin River Delta, and Klamath Basin, northern California—Five-year summary, 2013–17

Released July 23, 2019 14:26 EST

2019, Open-File Report 2019-1062

Ian A. Dwight, Peter S. Coates, Jessica H. Vogt, Joseph L. Atkinson, Joseph P. Fleskes, Daniel P. Connelly, Matt G. Meshriy, Scott C. Gardner, Simone T. Stoute, Maurice E. Pitesky

The U.S. Geological Survey Western Ecological Research Center, Pheasants Forever, Mandeville Island Duck Club, and the California Department of Fish and Wildlife collaborated in a reconnaissance study to monitor populations of ring-necked pheasant (Phasianus colchicus) using radio-telemetry in the Sacramento Valley, Sacramento-San Joaquin River Delta, and Klamath Basin of northern California. The purpose of this study was to provide agencies and private landowners with a framework of decision-support tools to help manage pheasant populations in California. During winter, spring, and autumn of 2013–17, we radio- or Global Positioning System-marked 227 female pheasant across six study sites. Data collection was focused on investigating nest-site and brood-rearing habitat selection, examining avian predator composition, and estimating population vital rates to improve our understanding of pheasant population dynamics and to identify factors that may contribute to decreases in pheasant populations in California. The cumulative annual adult survival probability across all sites during 2013–17 was 27.6 percent (95-percent confidence interval [CI], 21.9–33.6), and the cumulative nest and brood survival probabilities were 34.5 percent (95-percent CI, 27.0–42.2) and 54.2 percent (95-percent CI, 43.7–63.5), respectively. Evidence from microhabitat surveys completed at nest-sites, brood locations, and random locations suggested that marked female pheasant tended to select increasing vertical cover and residual vegetation cover and tended to avoid areas of increasing bare ground cover regardless of life-history stage. However, females at nest-sites selected increasing grass cover and height, whereas brood-rearing females tended to select increasing forb cover and height. Only perennial grass cover and perennial grass height were shown to have a positive influence on nest survival, which suggests that increasing perennial grass cover in areas occupied by pheasant may increase nest survival. Analysis of environmental factors linked to vital rate information are ongoing and will continue with investigations at increased spatial scales (that is, macro-habitat) to develop integrated population models that can incorporate abundance estimates from crow count data with vital rates from telemetry data. This report includes results from 5 years of data collection and should be interpreted with caution, as these findings are preliminary.

Preliminary methodology to assess the national and regional impact of U.S. wind energy development on birds and bats

Released July 23, 2019 14:11 EST

2015, Scientific Investigations Report 2015-5066

J.E. Diffendorfer, Julie A. Beston, Matthew D. Merrill, J.C. Stanton, M.D. Corum, Scott R. Loss, Wayne E. Thogmartin, Douglas H. Johnson, Richard A. Erickson, Kevin W. Heist

The U.S. Geological Survey has developed a methodology to assess the impacts of wind energy development on wildlife; it is a probabilistic, quantitative assessment methodology that can communicate to decision makers and the public the magnitude of these effects on species populations. The methodology is currently applicable to birds and bats, focuses primarily on the effects of collisions, and can be applied to any species that breeds in, migrates through, or otherwise uses any part of the United States. The methodology is intended to assess species at the national scale and is fundamentally different from existing methods focusing on impacts at individual facilities.

Publicly available fatality information, population estimates, species range maps, turbine location data, biological characteristics, and generic population models are used to generate both a ranked list of species based on relative risk as well as quantitative measures of the magnitude of the effect on species' population trend and size. Three metrics are combined to determine direct and indirect relative risk to populations. A generic population model is used to estimate the expected change in population trend and includes additive mortality from collisions with wind turbines. Lastly, the methodology uses observed fatalities and an estimate of potential biological removal to assess the risk of a decline in population size. Data for six bird species have been processed through the entire methodology as a test case, and the results are presented in this report.

Components of the methodology are based on simplifying assumptions and require information that, for many species, may be sparse or unreliable. These assumptions are presented in the report and should be carefully considered when using output from the methodology. In addition, this methodology can be used to recommend species for more intensive demographic modeling or highlight those species that may not require any additional protection because effects of wind energy development on their populations are projected to be small.

A Methodology to Assess the National and Regional Impacts of U.S. Wind Energy Development on Birds and Bats

Released July 23, 2019 14:04 EST

2019, Scientific Investigations Report 2018-5157

J.E. Diffendorfer, J.A. Beston, M.D. Merrill, J.C. Stanton, M.D. Corum, S.R. Loss, W.E. Thogmartin, D.H. Johnson, R.A. Erickson, K.W. Heist

This scientific investigations report describes an effort by the U.S. Geological Survey (USGS) that used research, monitoring data, and modeling to develop a methodology to assess both the current and future population-level consequences of wind energy development on species of birds and bats that are present in the United States during any part of their life cycle. The methodology is currently applicable to birds and bats, focuses primarily on the effects of collisions with turbines, and can be applied to any species that breeds in, migrates through, or otherwise uses any part of the United States. The methodology assesses species at the national and regional scales and identifies those species potentially in need of more detailed study, as well as those species that are likely at low risk from wind energy development. This approach is fundamentally different from existing methods focusing on impacts at individual facilities.

This report supersedes USGS Scientific Investigations Report 2015–5066 by the same authors, which described a preliminary version of the methodology. Following reviews of the preliminary methodology by a panel of external experts, public comments, and additional internal review, the methodology was revised and finalized.

The three components of the refined methodology described in this new report rely on publicly available fatality information, population estimates, species range maps, turbine location data, biological characteristics of species, and population models. First, three metrics are combined to determine direct and indirect relative effects from wind energy facilities to generate a list of species scores. Second, a generic population model estimates the expected change in population trend caused by the additive mortality from collisions with wind turbines. Third, the methodology combines an estimate of observed fatalities and an estimate of potential biological removal to assess the possibility of a decrease in population size. The latter two components are quantitative. In a test case, the methodology was used to analyze data for six bird species and three bat species.

Components of the methodology are based on simplifying assumptions and require information that, for many species, may be sparse or unreliable or may require further study. These assumptions should be carefully considered when using outputs from the methodology. Increases in the quality of data for fatalities from collisions with wind turbines, species distributions, abundance, and demography will likely improve results for uses of the methodology.

The methodology’s design identifies and prioritizes a subset of the bird and bat species that may experience population-level impacts from collisions with wind turbines, both currently and from future wind energy development in the United States. Results of an assessment using this methodology could focus future research to improve our understanding of those impacts and to guide avoidance and minimization strategies. In addition, this methodology can be used to identify species for more intensive demographic modeling or to highlight those species that may not require any additional research because effects of wind energy development on their populations are projected to be small. The effects of wind energy facilities on nine unidentified species used in the test case described in this report have not been assessed. Their data were simply used to show the application of the methodology to real-world data and the types of outputs it would produce.

The use of continuous water-quality time-series data to compute nutrient loadings for selected Iowa streams, 2008–17

Released July 23, 2019 13:34 EST

2019, Scientific Investigations Report 2019-5054

Jessica D. Garrett

In support of nutrient reduction efforts, nitrate (as nitrate plus nitrite) and phosphorus loads and yields were computed for selected streams in Iowa based on continuously monitored sensor data for 2008–17 and 2014–17, respectively. Sample data were used to assess nitrate sensor bias and to create phosphorus-turbidity surrogate models. Where needed, nitrate loads were corrected for site-specific sensor bias, which was determined to be as high as 9.25 percent. Nitrate loads presented in this report using continuous (generally 15-minute interval) data were on average 4 percent less, but as much as 38 percent less, than annual loads computed from daily mean nitrate concentrations not corrected for sensor bias. Streamflow-based phosphorus models had poorer fit (adjusted coefficient of determination values less than 0.75) than turbidity-based models (adjusted coefficient of determination approximately 0.9). However, alternate models based on streamflow were used to obtain a more complete annual phosphorus load despite seasonal and fragmentary sensor data.

Mean annual nitrate yields for 18 selected sites (96 site-years) ranged from 1.68 to 164 pounds per square mile per day (lb/mi2/d), compared to 19.4 lb/mi2/d average statewide yield needed to achieve the nitrate-reduction goal. Mean annual phosphorus yields for selected sites on the Maquoketa River, South Raccoon River, and West Nishnabotna River range from 1.57 to 7.19 lb/mi2/d, compared to 1.06 lb/mi2/d average statewide yield needed to achieve the phosphorus-reduction goal.

Natural hazards and mineral commodity supply: Quantifying risk of earthquake disruption to South American copper supply

Released July 23, 2019 12:10 EST

2019, Resources Policy

Emily Schnebele, Kishor Jaiswal, Nicolas Luco, Nedal T. Nassar

Mineral resources, and their mining and enrichment operations, are not equally distributed across Earth. The concentration of mineral supply in certain regions, owing to the geology or geography of the mineral resource, raises the level of risk related to supply disruption. Where mineral production coincides with areas prone to natural hazards, supply may be especially at risk. However, the level of risk that natural hazards pose to mineral supply has yet to be quantified on a global or regional scale. Using copper in South America as a case study, this paper offers methods for quantifying (i) the coincidence of mineral production and seismic hazards, and (ii) the Expected Annual Disruption (EAD) of the mineral supply from earthquakes. The first of these methods indicates that, of the 101 copper producing facilities in South America considered, 76 are located within an area of high seismic hazard, taken here as the area with>85% chance of exceeding Modified Mercalli Intensity VI earthquake shaking in 50 years. Collectively, the 76 facilities comprise 82%, 87%, and 91% of the 2015 South American mine production, smelter capacity, and refinery capacity, respectively. For each of the 101 facilities, the second method calculates the EAD using a full earthquake shaking hazard forecast at the location, the annualized copper production of the facility, and models of the vulnerability of that production to shaking. The EADs are summed by country, here within South America, as a demonstration of how supply risk could eventually be quantified globally. Consideration of two illustrative vulnerability models shows that future work is needed to determine percentages of disruption to mineral production for different levels of earthquake shaking. Ultimately, the methods presented herein could be applied to other mineral commodities and/or adapted for other natural hazards, and the resulting EADs could be summed. Results from these methods could be used to focus more detailed risk assessments where the risk is highest.

Geochronologic, isotopic, and geochemical data from igneous rocks in the Lane Mountain area, San Bernardino County, California

Released July 23, 2019 10:35 EST

2019, Open-File Report 2019-1070

Paul Stone, Howard J. Brown, M. Robinson Cecil, Robert J. Fleck, Jorge A. Vazquez, John A. Fitzpatrick, Jose J. Rosario

We present new geochronologic, isotopic, and geochemical data for selected igneous rocks in the Lane Mountain area, California. We determined SHRIMP-RG U-Pb zircon ages for the following units: (1) Larrea complex (~253 Ma and ~149–146 Ma); (2) Daisy granodiorite (~151 Ma); (3) Jack Spring quartz monzonite (~85–82 Ma); (4) unnamed porphyritic dikes and stocks (~80–73 Ma); and (5) Lane Mountain volcanics (~22 Ma). These results confirm and refine previous age determinations for the Larrea complex, Jack Spring quartz monzonite, and Lane Mountain volcanics, and provide the first reliable ages for the Daisy granodiorite and the unnamed porphyritic rocks. Sri of the plutonic rocks increases from ~0.704 to ~0.705–0.706 to ~0.708–0.709 for samples dated as ~250, ~150, and ~85–70 Ma, respectively, which indicates progressively greater involvement of Precambrian continental lithosphere in magma generation through time. The Sri and geochemical data suggest that the most significant change in magmatic source occurred between ~150 and 85 Ma.

Interactions of Human-Caused Mortality, Genetic Introgression, and Management among Wild Red Wolves: Developing Scientific Consensus

Released July 23, 2019 09:47 EST

2019, Report

Jaime Collazo

After being nearly driven to extinction by the combination of human persecution, human-caused habitat change, and subsequent hybridization with coyotes, red wolves (Canis rufus) were rescued from extinction by the establishment of a captive breeding program in 1973.  In 1987, red wolves were first released into a coyote-free (Canis latrans) area in northeastern North Carolina.  But by the early 1990’s coyotes began colonizing the area, and pairings between red wolves and coyotes were first detected in 1993.  In 2000, a program to contain hybridization and introgression by sterilizing coyotes and removing hybrids began.  Genetic assignment tests were used to determine which canids were red wolves, hybrids, and coyotes.  But despite these management efforts, the number of red wolves in the reintroduced population has remained around 100.  Given these additional sources of uncertainty surrounding hybridization and the potential increase in introgression along with the existing challenges for survival of red wolves as individuals and a species, the success of the recovery program remains unclear.  We propose an expert workshop to investigate, address, and seek scientific consensus for two primary interrelated questions at the source of the uncertainty: (a) how does human-caused mortality affect reproductive barriers among red wolves and coyotes; and (b) at what biological point should genetic introgression prompt the delisting of red wolves?  These two objectives are critical steps in the management process required to guide strategic planning and conservation for the species.

Preliminary report on engineering and geological effects of the July 2019 Ridgecrest earthquake sequence

Released July 23, 2019 09:45 EST

2019, Report

Scott J Brandenberg, Pengfei Wang, Chukwuebuka C Nweke, Kenneth Hudson, Silvia Mazzoni, Yousef Bozorgnia, Kenneth W. Hudnut, Craig A. Davis, Sean K Ahdi, Farzin Zareian, Jawad Fayaz, Richard D Koehler, Colin Chupik, Ian Pierce, Alana Williams, Sinan Akciz, Martin B Hudson, Tadahiro Kishida, Benjamin A. Brooks, Ryan D. Gold, Daniel J. Ponti, Katherine Scharer, Devin McPhillips, Christopher Duross, Todd Ericksen, Janis . Hernandez, Jay Patton, Brian Olson, Timothy E. Dawson, Jerome Treiman, Kelly Blake, Jeffrey Buchhuber, Chris L M Madugo, Joseph Sun, Andrea Donnellan, Greg Lyzenga, Erik Conway

Jonathan P. Stewart, editor(s)

The Ridgecrest Earthquake sequence included a foreshock event on July 4 2019 (M6.4) and a M7.1 mainshock event on July 5 2019. These events occurred in the Eastern California Shear Zone, near Indian Wells Valley, south of China Lake and west of Searles Valley. GEER has partnered with several organizations to collect perishable data and document the important impacts of these events, including the US Geological Survey, the California Geological Survey, the US Navy, the Southern California Earthquake Center, and local utilities. Critical geotechnical features of this event are extensive left-lateral (M6.4 event) and right-lateral (M7.1 event) surface ruptures over fault segments of variable complexity and width as well as across extensional and compressive step-over zones. We also document lifeline performance at fault crossings (gas, water, electrical), mainshock slip and afterslip, liquefaction and lateral spreading features, and liquefaction effects on structures. These effects are documented using field (ground) mapping and aerial imagery that will support subsequent development of high-resolution digital elevation models. Over 750 ground motions were recorded from the foreshock and mainshock alone, with many additional aftershock records. The data demonstrate significant impacts of site response and rupture directivity on ground motion attributes.

Science needs for continued development of total nitrogen deposition budgets in the United States

Released July 23, 2019 09:42 EST

2019, Report

Gregory A. Wetherbee, Pamela H. Templar, Richard V. Pouyat, Stephen M. Decina, Brian M. Kerschner, Thomas H. Whitlow, Pamela E. Padgett, Donna B. Schwede, Jill S. Baron, David Clow, M. Alisa Mast, Graham A. Sexstone, Kristi H. Morris

The objectives of this white paper are to describe the state of the science with respect to total Nr deposition budgets in North America and the research needed to improve these budgets from both a measurement and modeling standpoint. The document is intended to serve as a plan for TDep research activities but also, more broadly, to provide program managers, natural resource managers, policy makers and scientists with an understanding of the need for complete and accurate Nr deposition budgets to protect ecosystem health and human welfare, and the linkages between the underlying policy-relevant science questions and the specific knowledge and data gaps needed to improve Nr deposition budgets.

Monitoring storm tide, flooding, and precipitation from Hurricane Maria in Puerto Rico and the U.S. Virgin Islands, September 2017

Released July 23, 2019 08:40 EST

2019, Open-File Report 2019-1065

Michael J. Byrne Sr.

Hurricane Maria made landfall south of Yabucoa Harbor, Puerto Rico, as a category 4 hurricane with maximum sustained winds of 155 miles per hour on September 20, 2017. The hurricane devastated much of the U.S. Virgin Islands and Puerto Rico. The U.S. Geological Survey (USGS), in cooperation with Federal Emergency Management Agency, installed a temporary monitoring network of 13 water-level and barometric pressure sensors along the coast of Puerto Rico prior to the storm. In addition to the temporary sensors, the USGS maintains 99 permanent real-time streamgages and 36 real-time precipitation stations in Puerto Rico. The real-time data, updated hourly, during and after the hurricane are displayed in the USGS Flood Event Viewer (https://stn.wim.usgs.gov/FEV/#MariaSeptember2017) and in the USGS National Water Information System.

The USGS measured 181 coastal and riverine high-water marks throughout Puerto Rico after the storm. Water elevations are referenced to the Puerto Rico Vertical Datum of 2002 (PRVD02) and local datums in Puerto Rico and to the U.S. Virgin Islands Vertical Datum of 2009 (VIVD09) in the U.S. Virgin Islands. Data from the Hurricane Maria storm-tide network are available in tab-delimited, American Standard Code for Information Interchange (ASCII) format and Network Common Data Form (NetCDF) format by site for each sensor through the USGS Flood Event Viewer.

Water-budget analysis of the Upper Big Sandy Designated Ground-water Basin alluvial aquifer, Elbert, El Paso, and Lincoln Counties, Colorado, 2016

Released July 22, 2019 11:20 EST

2019, Scientific Investigations Report 2019-5049

Michael S. Kohn, Jeannette H. Oden, L. R. Arnold

The U.S. Geological Survey in cooperation with the Colorado Water Conservation Board and the Upper Big Sandy Groundwater Management District carried out a study in 2016 to evaluate potential groundwater storage changes within the Upper Big Sandy Designated Groundwater Basin (UBSDGB) alluvial aquifer, including groundwater flow between the UBSDGB alluvial aquifer and the Denver Basin bedrock aquifers. The UBSDGB alluvial aquifer is located along the ephemeral Big Sandy Creek on the east-central edge of the Denver Basin aquifer system and covers an area of about 66,560 acres within the UBSDGB. The UBSDGB alluvial aquifer consists of unconsolidated Quaternary sand and gravel deposits that contain an unconfined (water table) groundwater system. The western three-fourths of the UBSDGB alluvial aquifer overlies the Tertiary and Cretaceous bedrock formations that compose the Denver Basin aquifer system. The updated water budget for the UBSDGB alluvial aquifer, including annual change in groundwater storage in 2016, was determined by combining water-budget information from an existing Denver Basin model for about three-fourths of the study area with best estimates for the major water-budget components for the area outside the Denver Basin aquifer system. The western part of the UBSDGB was included in the Denver Basin model (modeled area), whereas the eastern part of the UBSDGB was not included in the Denver Basin model (unmodeled area). The water-budget components were first estimated for the modeled area using outputs from the Denver Basin model, which uses the modular finite-difference groundwater flow computer model MODFLOW-2000 with 1-mile grid cells. For this study, the Denver Basin model was updated with additional data from 2004 through 2016 to generate current (2016) estimates of water consumption in the UBSDGB alluvial aquifer. A basin-specific water budget for the UBSDGB alluvial aquifer from the Denver Basin model was computed using a modeling tool called ZONEBUDGET. The modeled area groundwater budget, along with previous studies, was used to estimate a groundwater budget for the unmodeled area, and results for the modeled and unmodeled areas were combined for an overall water-budget estimate for the entire UBSDGB alluvial aquifer.

The net groundwater flow into the basin from adjacent alluvial aquifers was positive with flow entering the UBSDGB alluvial aquifer. Combining the total inflow from adjacent alluvial and the total outflow to adjacent alluvial aquifers resulted in a net flow from adjacent alluvial aquifers to UBSDGB alluvial aquifer of 5,125 acre-feet (ac-ft) in 2016. The net flow between the underlying bedrock aquifers and the UBSDGB alluvial aquifer was positive with flow entering the UBSDGB alluvial aquifer from the bedrock aquifers. The net flow from the bedrock aquifers to the UBSDGB alluvial aquifer was 347 ac-ft in 2016. Net recharge (precipitation and irrigation return flows minus evaporation) into the UBSDGB alluvial aquifer was negative with groundwater being removed from the UBSDGB alluvial aquifer over the total area of the basin. Combining the total inflow from recharge to the UBSDGB alluvial aquifer of 11,153 ac-ft in 2016 and the total evapo-transpiration of −11,656 ac-ft from the UBSDGB alluvial aquifer in 2016 resulted in a net recharge from UBSDGB alluvial aquifer of −503 ac-ft in 2016. Combining the modeled and unmodeled well pumping resulted in a total well pumping volume of −3,735 ac-ft in 2016 from the UBSDGB alluvial aquifer. The net groundwater flow to the stream network in the basin was negative with flow discharging from the UBSDGB alluvial aquifer into streams. Combining the total inflow from streams and the total outflow to streams for the UBSDGB alluvial aquifer resulted in −1,032 ac-ft in 2016 that was lost to the stream network in the UBSDGB. The net groundwater flow out of the UBSDGB was negative with flow leaving the UBSDGB alluvial aquifer. Combining the total area inflow to the basin from upgradient areas and the total area outflow from the basin for the UBSDGB alluvial aquifer resulted in a net flow out of the basin of −2,300 ac-ft. In the annual groundwater budget for 2016, groundwater storage in the UBSDGB alluvial aquifer system was removed because annual groundwater outflows from storage exceeded groundwater inflows to storage; in other words, water was removed from storage to balance the annual water budget. Combining the net flow from storage for the modeled area of 73 ac-ft and the inflow from storage for the unmodeled area of 2,025 ac-ft resulted in a net positive flow from storage of the UBSDGB alluvial aquifer of 2,098 ac-ft.

Increased pumping since 1958 in the Denver and upper Arapahoe aquifers, not necessarily in the UBSDGB, has caused a change in flow from bedrock units, which were minor or non-contributors of inflow to the UBSDGB alluvial aquifer, to receiving outflow from the UBSDGB alluvial aquifer. Since 2000, aquifer storage has been an inflow component of the water budget, which means that outflow from the modeled area exceeded inflow for the UBSDGB alluvial aquifer. Increased recharge from wetter than average years could replenish the UBSDGB alluvial aquifer. From 2003 through 2016, 13 of the 25 observation wells completed in the UBSDGB alluvial aquifer had a decline in the groundwater-level elevation with an average decline of −2.21 feet, and 12 of the 25 observation wells had an increase in the groundwater-level elevation with an average increase of 1.54 feet. In general, wells at the eastern and western edges of the UBSDGB showed an increase in groundwater-level elevation that appears related to areas of groundwater discharge from the lower Dawson and Laramie-Fox Hills bedrock aquifers to the UBSDGB alluvial aquifer. The remaining wells exhibited water-level declines. Future work could include the development of a basin-specific model to serve as a basin management tool for modeling changes in groundwater levels and storage under various future groundwater recharge and withdrawal scenarios.

Volcanic hazards in the Pacific U.S. Territories

Released July 19, 2019 08:57 EST

2019, Fact Sheet 2019-3036

Gabrielle Tepp, Brian Shiro, William W. Chadwick

The Commonwealth of the Northern Mariana Islands, Guam, and American Samoa lie along the western side of the famed Pacific Ring of Fire. Here, the processes of active island and submarine volcanoes produce activity both underwater and in the atmosphere that poses potential hazards to the daily lives of residents and travelers. Since 2000, CNMI volcanoes have erupted six times, and one submarine volcano has been active in American Samoa.

Reactivity of As and U co-occurring in mine wastes in northeastern Arizona

Released July 19, 2019 07:33 EST

2019, Chemical Geology (522) 26-37

Johanna Blake, Sumant Avasarala, Abdul-Mehdi Ali, Michael Spilde, Juan S Lezama-Pacheco, Drew Latta, Kateryna Artyushkova, Anastasia G Ilgen, Christopher Shuey, Christopher Nez, Jose M Cerrato

The reactivity of co-occurring arsenic (As) and uranium (U) in mine wastes was investigated using batch reactors, microscopy, spectroscopy, and aqueous chemistry. Analyses of field samples collected in proximity to mine wastes in northeastern Arizona confirm the presence of As and U in soils and surrounding waters, as reported in a previous study from our research group. In this study, we measured As (<0.500 to 7.77 μg/L) and U (0.950 to 165 μg/L) in waters, as well as mine wastes (<20.0 to 40.0 mg/kg As and <60.0 to 110 mg/kg U) and background solids (<20.0 mg/kg As and <60.0 mg/kg U). Analysis with X-ray fluorescence (XRF) and electron microprobe show the co-occurrence of As and U with iron (Fe) and vanadium (V). These field conditions served as a foundation for additional laboratory experiments to assess the reactivity of metals in these mine wastes. Results from laboratory experiments indicate that labile and exchangeable As(V) was released to solution when solids were sequentially reacted with water and magnesium chloride (MgCl2), while limited U was released to solution with the same reactants. The predominance of As(V) in mine waste solids was confirmed by X-ray absorption near edge (XANES) analysis. Both As and U were released to solution after reaction of solids in batch experiments with HCO3. Both X-ray photoelectron spectroscopy (XPS) and XANES analysis determined the predominance of Fe(III) in the solids. Mössbauer spectroscopy detected the presence of nano-crystalline goethite, Fe(II) and Fe(III) in (phyllo)silicates, and an unidentified mineral with parameters consistent with arsenopyrite or jarosite in the mine waste solids. Our results suggest that As and U can be released under environmentally relevant conditions in mine waste, which is applicable to risk and exposure assessment.

A 3-year in-situ measurement of CO2 efflux in coastal wetlands: understanding carbon loss through ecosystem respiration and its partitioning

Released July 18, 2019 15:21 EST

2019, Wetlands 1-12

Xueyang Yu, Siyuan Ye, Linda Olsson, Mengjie Wei, Ken Krauss, Hans Brix

Understanding the link between ecosystem respiration (Reco) and its influential factors is necessary to evaluate the sources of gaseous carbon loss in coastal wetlands. Seablite (Suaeda salsa Pall.) is the main vegetation type pioneering temperate coastal wetlands in northeast China, and is generally an understudied wetland type. To evaluate the influence of environmental factors on Reco, a multi-year in-situ experiment was carried out during the growing seasons of 2012 to 2014. Total CO2 efflux was measured and separated further into soil microbial and belowground root respiration (Rs + r) and plant respiration (Rplant). Reco displayed strong seasonal variation, with effluxes as high as 845 to 1150 mg CO2 m−2 h−1 during summer months and as low as 32 to 111 mg CO2 m−2 h−1 during spring (when new shoots are sprouting) and fall (when plants are senescing) months. Aboveground plant structures contributed on average 79% to total plant biomass, and accounted for most of the Reco measured; i.e., 62–96% was associated as Rplant. Plant activity was strongly seasonal, accordingly driving Reco, with 1 g of soil-emergent S. salsa biomass (dry weight) producing approximately 1.58 mg CO2 per hour toward Reco during mid-summer. When water level was below the soil surface, Rs + r was exponentially correlated to air temperature. Because Reco for S. salsa marsh in the Liaohe Delta is controlled by plant growth cycles, inundation regime, and air temperature, this finding may be applied for national carbon budget estimation purposes from S. salsa wetlands throughout Northeast China and potentially close a key gap in understanding the role of this large wetland area in contributing to respiratory CO2 emissions globally.

Benthic community dynamics in Coyote Creek and Artesian Slough, southern San Francisco Bay, California, May 2016 to March 2018

Released July 18, 2019 14:35 EST

2019, Open-File Report 2019-1057

Kelly H. Shrader, Sarah A. Pearson, Francis Parchaso, Janet K. Thompson

The primary objective of this study is to quantify current (2016–18) benthic-community structure and function in the southern San Francisco Bay, and to compare those communities to the communities in the neighboring sloughs. The study area is inclusive of the area south of the Dumbarton Bridge including Coyote Creek and Artesian Slough.
The southern San Francisco Bay is a system dependent on phytoplankton as the base to the food web. Despite abundant nutrients, southern San Francisco Bay has had limited phytoplankton production in the last several decades owing to poor light conditions caused by high turbidities, and high grazing losses from the water column by benthic invertebrates and zooplankton. However, the balance of biogeochemical conditions during spring of most years accommodates a short phytoplankton bloom in the southern San Francisco Bay. This balance between available light, nutrients, and grazing has maintained the phytoplankton biomass in the southern San Francisco Bay at low levels relative to other high-nutrient urban estuaries. The role of benthic invertebrates during episodic spring events, as well as in other seasons, remains of great interest to water-quality and biological resource managers.

Assessment of polycyclic aromatic hydrocarbon concentrations in southern Lake Powell, Glen Canyon National Recreation Area, Arizona and Utah, 2016–17

Released July 18, 2019 14:25 EST

2019, Scientific Investigations Report 2019-5065

Alissa L. Coes, Nicholas V. Paretti, David A. Alvarez, Jamie P. Macy

Polycyclic aromatic hydrocarbon contamination related to boat use is one of the most important water-quality issues affecting Lake Powell. High concentrations of polycyclic aromatic hydrocarbons in water are common around marinas and other areas with extensive motorboat activity because of releases of uncombusted or partially combusted oil and gasoline from boat engines. The fate of these compounds in Lake Powell is of serious environmental concern because of their toxicity and carcinogenicity and their moderate persistence once they enter the aquatic ecosystem. In 2016–17, the U.S. Geological Survey (USGS) assessed the presence and concentrations of polycyclic aromatic hydrocarbons in Lake Powell at seven sites where concentrations have historically been elevated and one site where concentrations have historically been relatively low. Semipermeable membrane devices were used to collect samples that represent time-weighted averages of polycyclic aromatic hydrocarbon concentrations in water over one-month deployment periods. Samples were collected from the epilimnion of the lake at each of the eight sampling sites during two periods of relatively high boat use (summer), and one period of relatively low boat use (spring). Twenty-eight out of 33 polycyclic aromatic hydrocarbons analyzed were detected in Lake Powell during the three sampling events. During the two summer sampling events, concentrations were generally higher, and more compounds were detected, than during the spring sampling event. Twenty-two of the polycyclic aromatic hydrocarbons analyzed in 2016–17 had previously been analyzed by the USGS in the summer of 2010 at the same 8 sites using the same collection method. Eleven of 22 compounds were detected in the summer 2010, summer 2016, and summer 2017 sampling events, and 1 was detected in the summer 2010 and summer 2017 samplings, but not in the summer 2016 sampling event. During both the current and previous sampling events, concentrations were generally higher, and more compounds were detected, at the high-use marina sites located most downstream on the lake. The consistent presence of a wide range of polycyclic aromatic hydrocarbons in the water of Lake Powell indicates chronic and (or) recent anthropogenic sources of contamination. The results from this study will provide the National Park Service with information necessary to determine if the current regulations on emission standards for personal watercraft used on Lake Powell are effective in lowering polycyclic aromatic hydrocarbon concentrations in the lake.

An introduction to the “Oceans and Society: Blue Planet” Initiative

Released July 17, 2019 14:47 EST

2019, Journal of Operational Oceanography

Emily A Smail, Paul DiGiacomo, Sophie Seeave, Samy Djavidnia, Louis Celliers, Pierre-Yves Le Traon, Jeremy Gault, Elva Escobar-Briones, Hans-Peter Plag, Christine Pequignet, Lenore Bajona, Lin Zhang, Jay Pearlman, Andy Steven, Jon Hodge, Fanny-Mae Racault, Curt D. Storlazzi, Willam Skirving

We live on a blue planet, and Earth’s waters benefit many sectors of society. The future of our blue planet is increasingly reliant on the services delivered by marine, coastal and inland waters and on the advancement of effective, evidence-based decisions on sustainable development. “Oceans and Society: Blue Planet” (hereafter denoted as “GEO Blue Planet”) is an initiative of the Group on Earth Observations (GEO) that aims to ensure the sustained development and use of ocean and coastal observations for the benefit of society. GEO Blue Planet works to advance and exploit synergies among the many observational programmes devoted to ocean and coastal waters; to improve engagement with a variety of stakeholders for enhancing the timeliness, quality and range of information delivered; and to raise awareness of the societal benefits of ocean observations at the public and policy levels. This paper summarizes the role of GEO Blue Planet, current activities and considerations for future directions.

Wildland fire science at the U.S. Geological Survey—supporting wildland fire and land management across the United States postcard

Released July 17, 2019 09:30 EST

2019, General Information Product 190

Paul F. Steblein, Mark P. Miller, Suzanna C. Soileau

The U.S. Geological Survey’s Wildland Fire Science Program produces information to identify the causes of wildfires, understand the impacts and benefits of both wildfires and prescribed fires, and help prevent and manage larger, catastrophic events. USGS fire scientists provide information and develop tools that are widely used by stakeholders to make decisions before, during, and after wildfires in desert, grassland, tundra, wetland, and forest ecosystems across the United States. Active areas of research include—

  • Wildland fire behavior and risk management
  • Fire ecology, fire effects, and post-fire restoration of ecosystems
  • Risk assessments for human health, public safety, and the Nation’s infrastructure
  • Remote sensing and geospatial tools and data.

FLUXNET-CH4 Synthesis Activity: Objectives, observations, and future directions

Released July 17, 2019 08:57 EST

2019, Bulletin of the American Meteorological Society

Sara H. Knox, Robert B. Jackson, Benjamin Poulter, Gavin McNicol, Etienne Fluet-Chouinard, Zheng Zhang, Gustaf Hugelius, Philippe Bousquet, Josep G Canadell, Marielle Saunois, Dario Papale, Housen Chu, Trevor F. Keenan, Dennis Baldocchi, Margaret S Torn, Ivan Mammarella, Carlo Trotta, Mika Aurela, Gil Bohrer, David I Campbell, Alessandro Cescatti, Samuel D. Chamberlain, Jiquan Chen, Weinan Chen, Sigrid Dengel, Ankur R. Desai, Eugenie S Euskirchen, Thomas Friborg, Daniele Gasbarra, Ignacio Goded, Mathias Goeckede, Martin Heimann, Manuel Helbig, Takashi Hirano, David Y. Hollinger, Hiroki Iwata, Minseok Kang, Janina Klatt, Ken Krauss, Lars Kutzbach, Annalea Lohila, Bhaskar Mitra, Timothy H Morin, Mats B Nilsson, Shuli Niu, Asko Noormets, Walter C. Oechel, Matthias Peichl, Olli Peltola, Michele L. Reba, Andrew D. Richardson, Benjamin R K Runkle, Youngryel Ryu, Torsten Sachs, Karina V R Schäfer, Hans Peter Schmid, Narasinha Shurpali, Oliver Sonnentag, Angela C I Tang, Masahito Ueyama, Rodrigo Vargas, Timo Vesala, Eric Ward, Lisamarie Windham-Myers, Georg Wohlfahrtd, Donatella Zona

Here we describe a new coordination activity and initial results for a global synthesis of eddy covariance CH4 flux measurements. This paper describes the formation of, and initial results for, a new FLUXNET coordination network for ecosystem-scale methane (CH4) measurements at 60 sites globally, organized by the Global Carbon Project in partnership with other initiatives and regional flux tower networks. The objectives of the effort are presented along with an overview of the coverage of eddy covariance (EC) CH4 flux measurements globally, initial results comparing CH4 fluxes across the sites, and future research directions and needs. Annual estimates of net CH4 fluxes across sites ranged from -0.2 ± 0.02 g C m-2 y-1 for an upland forest site to 114.9 ± 13.4 g C m-2 y-1 for an estuarine freshwater marsh, with fluxes exceeding 40 g C m-2 y-1 at multiple sites. Average annual soil and air temperatures were found to be the strongest predictor of annual CH4 flux across wetland sites globally. Water table position was positively correlated with annual CH4 emissions, although only for wetland sites that were not consistently inundated throughout the year. The ratio of annual CH4 fluxes to ecosystem respiration increased significantly with mean site temperature. Uncertainties in annual CH4 estimates due to gap filling and random errors were on average ± 1.6 g C m-2 y-1 at 95% confidence, with the relative error decreasing exponentially with increasing flux magnitude across sites. Through the analysis and synthesis of a growing EC CH4 flux database, the controls on ecosystem CH4 fluxes can be better understood, used to inform and validate Earth system models, and reconcile differences between land-surface model- and atmospheric-based estimates of CH4 emissions.

Hydroacoustic, meteorologic and seismic observations of the 2016 Nansen Ice Shelf calving event and iceberg formation

Released July 16, 2019 14:04 EST

2019, Frontiers in Earth Science (7)

Robert Dziak, W. S. Lee, Joe Haxel, Haru Matsumoto, Gabrielle Tepp, T-K Lau, Lauren Roche, S H Yun, C. K. Lee, J.Y. Lee, S.T. Yoon

On 7 April 2016, the Nansen Ice Shelf (NIS) front calved into two icebergs, the first large-scale calving event in >30 years. Three hydrophone moorings were deployed seaward of the NIS in December 2015 and over the following months recorded hundreds of short duration, broadband (10-400 Hz) cryogenic signals, likely caused by fracturing of the ice-shelf. The majority of these icequakes occur between January and early March 2016, several weeks prior to the calving observed by satellite on 7 April. Barometric pressure and wind speed records show the day the icebergs drifted from the NIS coincided with the largest low-pressure storm system recorded in the previous 7 months. A nearby seismic station also shows an increase in low-frequency energy, harmonic tremor, and microseisms on 7 April. Our interpretation is the northern segment of the NIS leading edge broke free during mid-January to February, producing high acoustic energy, but the icebergs remained stationary until the combination of a strong low-pressure system, with high winds freed the icebergs. As the unpinning of Antarctic ice shelves is not a well-documented process, our observations show that storm systems may play an under-appreciated role in Antarctic ice shelf break-up.

Guidelines for determining flood flow frequency—Bulletin 17C

Released July 16, 2019 10:55 EST

2019, Techniques and Methods 4-B5

John F. England Jr., Timothy A. Cohn, Beth A. Faber, Jery R. Stedinger, Wilbert O. Thomas Jr., Andrea G. Veilleux, Julie E. Kiang, Robert R. Mason Jr.

Accurate estimates of flood frequency and magnitude are a key component of any effective nationwide flood risk management and flood damage abatement program. In addition to accuracy, methods for estimating flood risk must be uniformly and consistently applied because management of the Nation’s water and related land resources is a collaborative effort involving multiple actors including most levels of government and the private sector.

Flood frequency guidelines have been published in the United States since 1967, and have undergone periodic revisions. In 1967, the U.S. Water Resources Council presented a coherent approach to flood frequency with Bulletin 15, “A Uniform Technique for Determining Flood Flow Frequencies.” The method it recommended involved fitting the log-Pearson Type III distribution to annual peak flow data by the method of moments.

The first extension and update of Bulletin 15 was published in 1976 as Bulletin 17, “Guidelines for Determining Flood Flow Frequency” (Guidelines). It extended the Bulletin 15 procedures by introducing methods for dealing with outliers, historical flood information, and regional skew. Bulletin 17A was published the following year to clarify the computation of weighted skew. The next revision of the Bulletin, the Bulletin 17B, provided a host of improvements and new techniques designed to address situations that often arise in practice, including better methods for estimating and using regional skew, weighting station and regional skew, detection of outliers, and use of the conditional probability adjustment.

The current version of these Guidelines are presented in this document, denoted Bulletin 17C. It incorporates changes motivated by four of the items listed as “Future Work” in Bulletin 17B and 30 years of post-17B research on flood processes and statistical methods. The updates include: adoption of a generalized representation of flood data that allows for interval and censored data types; a new method, called the Expected Moments Algorithm, which extends the method of moments so that it can accommodate interval data; a generalized approach to identification of low outliers in flood data; and an improved method for computing confidence intervals.

Federal agencies are requested to use these Guidelines in all planning activities involving water and related land resources. State, local, and private organizations are encouraged to use these Guidelines to assure uniformity in the flood frequency estimates that all agencies concerned with flood risk should use for Federal planning decisions.

This revision is adopted with the knowledge and understanding that review of these procedures will be ongoing. Updated methods will be adopted when warranted by experience and by examination and testing of new techniques.

Triangle area water supply monitoring project, North Carolina-Summary of monitoring activities, quality assurance, and data, October 2015–September 2017

Released July 16, 2019 09:15 EST

2019, Open-File Report 2019-1077

C.A. Pfeifle, J.L. Cain, R.B. Rasmussen

Surface-water supplies are important sources of drinking water for residents in the Triangle area of North Carolina, which is located within the upper Cape Fear and Neuse River Basins. Since 1988, the U.S. Geological Survey and a consortium of local governments have tracked water-quality conditions and trends in several of the area’s water-supply lakes and streams. This report summarizes data collected through this cooperative effort, known as the Triangle Area Water Supply Monitoring Project, during October 2015 through September 2016 (water year 2016) and October 2016 through September 2017 (water year 2017). Major findings for this period include the following:

  • More than 5,000 individual measurements of water quality were made at a total of 20 sites—7 in the Neuse River Basin and 13 in the Cape Fear River Basin. Only the measurements from the photic zone and 1 meter below the water surface are documented in this report.
  • Twenty-nine water-quality properties or constituents are presented in this report; State water-quality thresholds exist for 11 of these.
  • All observations met State water-quality thresholds for hardness, chloride, fluoride, sulfate, and nitrate plus nitrite.
  • North Carolina water-quality thresholds were exceeded one or more times for dissolved oxygen, dissolved-oxygen percent saturation, pH, water temperature, turbidity, and chlorophyll a.

Biocrust science and global change

Released July 15, 2019 14:30 EST

2019, New Phytologist (223) 1047-1051

Sasha C. Reed, Manuel Delgado-Baquerizo, Scott Ferrenberg

Global environmental changes such as climate and land‐use change affect ecosystems worldwide, and this New Phytologist Virtual Issue brings together fundamental research questions and novel approaches associated with the study of biological soil crusts in the context of such shifts. In a changing world, organisms can display a limited set of responses that will determine their persistence over varied spatial and temporal scales. Specifically, organisms might tolerate the change – for example, via phenotypic plasticity – and remain present in local communities. Alternatively, organisms might shift or retract their range to match their historical niche, they may adapt to the directional selection pressures imposed by change, or they could be driven to local (and possibly global) extinction. Efforts to understand which of these responses particular plant species or assemblages will exhibit are necessary for predicting changes in ecosystem functioning and trophic interactions under global change scenarios, and for managing and supporting sustainable terrestrial ecosystems. Accordingly, the assessment of plant responses to global change has become a significant research focus. Despite this impressive effort, our understanding and combined work to measure the responses to global change for species and communities of nonvascular autotrophs, such as the cyanobacteria, lichens, and bryophytes that form biological soil crusts (Fig. 1), remain rare compared with the large focus on vascular plants (Fig. 2; Reed et al., 2016). Nevertheless, these nonvascular photosynthetic communities and their responses to change could have critical implications for determining ecosystem structure and function at the global‐scale (Elbert et al., 2012; Ferrenberg et al., 2017; Rodriguez‐Caballero et al., 2018).

Assessment of continuous oil resources in the Eastern Great Basin Province of Nevada, Utah, and Idaho, 2018

Released July 15, 2019 13:15 EST

2019, Fact Sheet 2019-3002

Christopher J. Schenk, Tracey J. Mercier, Cheryl A. Woodall, Thomas M. Finn, Stephanie B. Gaswirth, Kristen R. Marra, Phuong A. Le, Michael E. Brownfield, Heidi M. Leathers-Miller, Ronald M. Drake II, Scott A. Kinney

The U.S. Geological Survey (USGS) quantitatively assessed the potential for undiscovered, technically recoverable continuous oil and gas resources in the Eastern Great Basin Province (Anna and others, 2007) of Nevada, Utah, and Idaho (fig. 1). The assessment focused on the area of the province between the Roberts Mountains and Sevier thrust systems (Peterson, 1994). The major petroleum source rocks within this area are the Upper Devonian–Lower Mississippian Pilot Shale and the Mississippian Chainman Formation (Gutschick and Rodriquez, 1979; Poole and Claypool, 1984; Giles, 1994; Trexler and others, 1995). The geologic model applied to the Pilot Shale and shales in the Chainman Formation is for these shales to have achieved generative maturity for oil by burial to at least 8,700 feet (2,652 meters) within some of the Neogene extensional basins (Grabb, 1994; Anna and others, 2007). Areas that satisfy this depth requirement were defined using modeled gravity data that were calibrated to the petroleum system in Railroad Valley and Pine Valley in Nevada (Barker and Peterson, 1991; Ïnan and Davis, 1994; Meissner, 1995; Anna and others, 2007). 

Offshore shallow structure and sediment distribution, Point Sur to Point Arguello, central California

Released July 15, 2019 09:47 EST

2019, Open-File Report 2018-1158

Samuel Y. Johnson, Stephen R. Hartwell, Janet T. Watt, Jeffrey W. Beeson, Peter Dartnell

This publication consists of three map sheets that display shallow geologic structure, along with sediment distribution and thickness, for an about 225-km-long offshore section of the central California coast between Point Sur and Point Arguello. Each map sheet includes three maps, at scales of either 1:150,000 or 1:200,000, as well as a set of figures that contain representative high-resolution seismic-reflection profiles. The maps and seismic-reflection surveys cover most of the continental shelf in this region. In addition, the maps show the locations of the shelf break and the 3-nautical-mile limit of California’s State Waters.

The seismic-reflection data, which are the primary dataset used to develop the maps, were collected to support the California Seafloor Mapping Program and U.S. Geological Survey Offshore Geologic Hazards projects. In addition to the three map sheets, this publication includes geographic information system data files of interpreted faults, folds, sediment thicknesses, and depths-to-base of sediment. The faults and folds shown on the maps have been locally simplified as appropriate for the map scales.

The right-lateral San Gregorio–Hosgri Fault (SGHF) is the most significant structure in the map area. On a regional scale, the SGHF is part of a 400-km-long, right-lateral fault system that extends northwestward from Point Arguello to the area offshore of San Francisco, where it merges with the San Andreas Fault. From north to south in this part of central California, the SGHF lies offshore between the south flank of Point Sur and the north flank of Point Piedras Blancas, then comes onshore at Point Piedras Blancas, before heading offshore again between the south flank of Point Piedras Blancas and Point Arguello. Cumulative fault offset along the SGHF is as much as 150 to 160 km, decreasing to the south by transferring slip on to northwest-striking faults that converge with the SGHF both onland and offshore from the east. In the map area, the offshore-converging faults include the Los Osos Fault, the Shoreline–Point Buchon Fault, the Casmalia Fault, and the Lions Head Fault.

Quaternary sediments and bedrock underlie the shelf. On the seismic-reflection profiles, we divide Quaternary shelf sediments into two units. Characterizing the younger, upper unit is a focus of this publication. This unit is inferred to have been deposited on the shelf in the last about 21,000 years during the sea-level rise that followed the last major lowstand and the Last Glacial Maximum (LGM). This upper unit overlies a transgressive surface of erosion, a commonly angular, wave-cut unconformity, and is generally characterized by low-amplitude, continuous to moderately continuous, diffuse, subparallel, generally flat reflections. Maps in this publication show both the thickness of this upper sediment unit and the depth to the base of the sediment unit. Within the map region, 11 different “domains” of post-LGM shelf sediment are delineated on the basis of sediment thickness and coastal geomorphology. Maximum sediment thickness is in the southern part of the region, offshore of the mouths of the Santa Ynez and Santa Maria Rivers. Minimum sediment thickness is found offshore of prominent rocky points, including Point Buchon and Piedras Blancas. Mean sediment thickness for the entire shelf in the map area between Point Sur and Point Arguello is 12.2 m, and total sediment volume is 24.7 million cubic meters.

Environmental DNA assays for invasive populations of the Black Carp, Mylopharyngodon piceus, in North America

Released July 13, 2019 14:23 EST

2019, Transactions of the American Fisheries Society

Xin Guan, E.M. Monroe, K.D. Bockrath, Erica L. Mize, C.B. Rees, Denise L. Lindsay, Kelly L. Baerwaldt, Leo Nico, Richard F. Lance

The Black Carp, Mylopharyngodon piceus, is an increasingly widespread invasive species in North America that threatens freshwater mussel populations. We developed four qPCR assays for detecting environmental DNA (eDNA) from these Black Carp populations. Assays were designed to target four mitochondrial DNA loci and were based on 34 complete mitochondrial genome sequences, including 29 generated in this study from samples obtained in three countries. Assays were validated for taxon specificity with in silico comparisons against archived DNA sequences and with in vitro tests of 41 DNA samples from Black Carp, as well as DNA samples from 30 non‐target fish species, all from the Mississippi River Basin. All four assays were able to detect the DNA of all Black Carp samples and did not exhibit any positive results with DNA from other tested species. Tests conducted in round‐robin fashion among three different laboratories found that all four assays were able to detect DNA at very low template concentrations (limits of detection = 3 copies/qPCR, limits of quantification = 16‐64 copies/qPCR) and, as part of in situ validation, were successful in detecting eDNA from Black Carp in aquaculture ponds. Despite some challenges with other attempts at in situ validation, the assays were also effective in detecting Black Carp eDNA in water samples from a drainage ditch in the upper reaches of the species’ range that was known to contain juvenile Black Carp, as well as in water samples from the Missisippi River and a connected oxbow lake in the lower reaches of the species range.

Diel feeding behavior in a partially migrant Mysis population: A benthic-pelagic comparison

Released July 13, 2019 09:28 EST

2019, Food Webs (20)

Brian O'Malley, Jason D. Stockwell

Populations that exhibit partial migration include migrants and non-migrants. For benthic-pelagic organisms that exhibit partial diel vertical migration (PDVM), migrants and non-migrants spend different amounts of time in benthic and pelagic foraging arenas over a diel cycle. For example, mysids exhibit PDVM and can feed on benthic and pelagic resources. Migratory individuals are assumed to undergo vertical migration at night to access pelagic food when predation risk is low. However, feeding behavior of non-migrant benthic individuals is not well understood. One hypothesis to explain individual variability in diel vertical migration (DVM) behavior is the hunger-satiation state of individuals (hunger-satiation (HS) hypothesis), which predicts that migration is driven by hunger and non-migration is a response to satiation. We assessed diel feeding patterns of benthic- and pelagic-caught Mysis in Lake Champlain to evaluate if PDVM was consistent with predictions of the HS hypothesis. Stomach fullness and diet composition revealed little diel difference in stomach contents between time of day or between benthic and pelagic individuals at night. Pelagic individuals had consistently higher stomach fullness shortly after sunset compared to near midnight. Non-migrant benthic individuals at night and benthic-caught individuals during the day had similar amounts of detritus in stomachs. High stomach fullness and levels of zooplankton in benthic-caught stomachs indicate Mysis actively feed when benthic, regardless of time of day. Our results suggest variation in Mysis migration behavior is not likely due to hunger-satiation, and highlights the importance of variable behavior in determining Mysis effects on food web interactions in deep lakes.

Crustal architecture beneath the southern Midcontinent (USA) and controls on Mesoproterozoic iron-oxide mineralization from 3D geophysical models

Released July 12, 2019 15:23 EST

2019, Ore Geology Reviews (Online First)

Anne E. McCafferty, Jeffrey D. Phillips, Albert H. Hofstra, Warren C. Day

Several types of critical mineral-bearing ore deposits in the southern Midcontinent region of the U.S. are hosted in Mesoproterozoic igneous rocks largely concealed beneath Paleozoic cover. Discerning the architecture of igneous intrusions and volcanic centers in the crust is fundamental to understanding the geologic evolution of this vast region and its mineral resources. To advance the understanding of the geologic framework beneath the Southeast Missouri Iron Metallogenic Province, we invert continental-scale magnetic and gravity anomaly data to three-dimensional (3D) physical property models. The regional models image altered and mineralized igneous rocks near the Precambrian basement surface and underlying intrusive complexes that extend down to the Moho. At shallow crustal levels, our models confirm that iron oxide-apatite ± rare earth element (IOA±REE) deposits and iron oxide-copper-gold ± cobalt (IOCG) deposits occur within or near the edges of large low density/low susceptibility early Mesoproterozoic (ca 1.4 Ga) silicic calderas and (ca 1.3 Ga) granitic plutons. Previous isotopic and geochemical studies conclude that the iron deposits and their volcanic host rocks originated from mantle-derived and crustal melts that erupted during regional extension. Extension was associated with thermal event(s) that produced the large-scale silicic magmatism related to the ca 1.45 Ga Eastern Granite Rhyolite Province (EGRP) and the 1.35 Ga Southern Granite Rhyolite Province (SGRP). We postulate that early in the evolution of the EGRP, several trans-crustal magmatic plumbing systems developed that are evident in the 3D models. The Southeast Missouri Metallogenic Province is underlain by one such magmatic system that is expressed as a northwest-trending ~ 50 km-wide by 200 km-long elongate track of high susceptibility at deep crustal levels. The high susceptibility corridor splays upward through the crust to the Precambrian surface where the iron deposits are the epigenetic manifestation of this magmatic event. Our findings confirm that the iron deposits, with no distinct connection at the surface, are connected to one large magmatic system at depth. We propose that other similar susceptibility tracks, which are present along the top of the mantle, mark additional feeder zones that allowed magma to ascend to the main eruptive centers that produced the Granite Rhyolite Provinces. The early Mesoproterozoic extensional tectonic framework established crustal-scale pathways that controlled the distribution of subsequent magmatic activity, including the ca 1.4 Ga calderas and underlying intrusions, ca 1.3 Ga silicic plutons and Phanerozoic alkaline intrusions. If these interpretations are correct, our study has identified large areas that are prospective for critical mineral-bearing ore deposits and, importantly, suggests that the Mesoproterozoic architecture may have influenced subsequent magmatism and hydrothermal activity in the southern Midcontinent of the U.S.

Spatiotemporal variability in energetic condition of alewife and round goby in Lake Michigan

Released July 12, 2019 14:05 EST

2019, Canadian Journal of Fisheries and Aquatic Sciences

David Bunnell, Steven A. Pothoven, Patricia Armenio, Lauren A. Eaton, David Warner, Ashley K. Elgin, Lyuba E. Burlakova, Alexander Y. Karatayev

Pelagic-oriented alewife (Alosa pseudoharengus) and benthic-oriented round goby (Neogobius melanostomus) are two important prey fishes in the Laurentian Great Lakes. In 2015, we evaluated their seasonal total energy (TE) across nine Lake Michigan transects. Round goby contained at least 48% more kilojoules of TE than alewife of equal length during spring and summer. TE varied spatially for both species, but only large alewife exhibited a consistent pattern, with higher values along the eastern shoreline. Variation in TE was not explained by site-specific prey densities for either species. Round goby energy density (ED) was higher in Lake Michigan than in central Lake Erie, but comparable to other regions of the Great Lakes. Alewife ED in 2015 was similar to that in 2002–2004 in Lake Michigan, with the exception of November (small alewife ED was 21% higher) and April (large alewife ED was 30% lower). Despite oligotrophication, our study suggests that starvation of juvenile and adults has not been directly contributing to overall declining prey fish abundance, although future research should evaluate the potential for overwinter starvation.

Improving population estimates of threatened spectacled eiders: Correcting aerial counts for visibility bias

Released July 11, 2019 14:58 EST

2019, Endangered Species Research (39) 191-206

Tyler Lewis, Michael Swaim, Joel A. Schmutz, Julian Fischer

Listed as threatened under the Endangered Species Act in 1993, the Spectacled Eider (Somateria fischeri) population in western Alaska has since rebounded, prompting an assessment of their suitability for delisting. This assessment, however, is limited by aerial-based population estimates that are incompletely corrected for unobserved eiders. Notably, aerial counts of eiders are corrected with a visibility correction factor (VCF), calculated as the ratio of ground-based nest counts to aerial pair counts, which disregards spatial variation in eider density. Accordingly, we (1) stratified our study area into zones of low, medium, and high eider density, (2) developed density-adjusted VCFs for each stratum, (3) evaluated the influence of several ecological factors on VCFs, and (4) estimated eider population size using our density-adjusted VCFs. For the low-density stratum, we estimated a VCF (± SE) of 1.35 ± 0.15, indicating that aerial counts of eider pairs closely matched ground counts of nests. In medium and high-density strata, VCFs increased to 2.46 ± 0.17 and 3.09 ± 0.19, respectively, suggesting that aerial detection decreased as eider densities increased. VCFs also increased for surveys that occurred late relative to nest initiation. Population estimates produced with our density-adjusted VCFs were 42% (5580 eiders) lower, on average, than those produced with the traditional VCF, which is currently used. Such large differences underscore the importance of accounting for density when correcting counts for incomplete detection, and, for threatened species such as Spectacled Eiders, may determine whether populations retain protected status.

Effects of manure and tillage on edge-of-field phosphorus loss in seasonally frozen landscapes

Released July 11, 2019 14:17 EST

2019, Journal of Environmental Quality (48) 966-977

Zachariah P. Zopp, Matthew D. Ruark, Anita M. Thompson, Todd D. Stuntebeck, Eric Cooley, Amber Radatz, Timothy Radatz

Environmental conditions and management practices affect nutrient losses in surface runoff, but their relative impacts on phosphorus (P) loss during frozen and nonfrozen ground periods have not been well quantified. More specifically, the relative importance of manure application, tillage, and soil-test P (STP) has not been assessed at the field scale. In this study, we compiled a dataset composed of 125 site-years of data from 26 fields that were continually monitored for edge-of-field P loss during snowmelt and storm events. Regression tree analyses were performed to rank the level of influence each environmental and management factor had on nutrient loads. Dissolved P (DP) was the majority of the total P (TP) during frozen conditions, but a small portion of TP during nonfrozen conditions. Manure application had a greater influence on the flow-weighted mean concentrations (FWMCs) of TP and DP during frozen conditions than during nonfrozen conditions. No-till resulted in greater TP and DP FWMCs during frozen conditions than conventional tillage, whereas the opposite effect for TP FWMC was seen during nonfrozen conditions. However, regression tree analysis revealed that STP (0- to 5-cm depth) was the most important factor in predicting DP and TP FWMCs during frozen conditions and DP FWMC during nonfrozen conditions. Extremely high STP values were associated with late-frozen manure applications and grazed pastures. Reducing surface P loss in seasonally frozen landscapes will require prioritizing management strategies that avoid manure application through early- and late-frozen conditions and lead to a drawdown of STP, particularly in the top 5 cm.

Water-quality, bed-sediment, and biological data (October 2016 through September 2017) and statistical summaries of data for streams in the Clark Fork Basin, Montana

Released July 11, 2019 08:14 EST

2019, Open-File Report 2019-1060

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

Water, bed sediment, and biota were sampled in selected streams from Butte to near Missoula, Montana, as part of a monitoring program in the Clark Fork Basin of western Montana. The sampling program was led by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, to characterize aquatic resources in the Clark Fork Basin and emphasize trace elements associated with historic mining and smelting activities. Sampling sites were on the Clark Fork and selected tributaries. Water samples were collected periodically at 20 sites from October 2016 through September 2017. Bed-sediment and biota samples were collected once at 13 sites during August 2017.

This report presents the analytical results and quality-assurance data for water-quality, bed-sediment, and biota samples collected at sites from October 2016 through September 2017. Water-quality data include concentrations of selected major ions, dissolved organic carbon, turbidity, nitrogen (nitrate plus nitrite), trace elements, and suspended sediment. Seasonal daily values of turbidity were determined at four sites. Bed-sediment data include trace-element concentrations in the fine-grained (less than 0.063 millimeter) fraction. Biological data include trace-element concentrations in whole-body tissue of aquatic benthic insects. Statistical summaries of water-quality, bed-sediment, and biological data for sites in the Clark Fork Basin are provided for the period of record.

Heat flow in the Western Arctic Ocean (Amerasian Basin)

Released July 10, 2019 15:19 EST

2019, Journal of Geophysical Research B: Solid Earth (Online First)

Carolyn D. Ruppel, A.H. Lachenbruch, Deborah Hutchinson, Robert Munroe, David Mosher

From 1963 to 1973 the U.S. Geological Survey (USGS) measured heat flow at 356 sites in the Amerasian Basin (Western Arctic Ocean) from a drifting ice island (T-3). The resulting measurements, which are unevenly distributed on Alpha-Mendeleev Ridge (AMR) and in Canada and Nautilus basins, greatly expand available heat flow data for the Arctic Ocean. Average T-3 heat flow is ~54.7 ± 11.3 mW m-2, and Nautilus Basin, including Mendeleev Plain, is the only well-surveyed area (~13% of data) with significantly higher average heat flow (63.8 mW m-2). Heat flow and bathymetry are not correlated at a large scale, and turbiditic surficial sediments (Canada and Nautilus basins) have higher heat flow than the sediments that blanket the AMR. Thermal gradients are mostly near-linear, implying that conductive heat transport dominates and that near-seafloor sediments are in thermal equilibrium with overlying bottom waters. Combining the heat flow data with modern seismic imagery suggests that some of the observed heat flow variability may be explained by local changes in sediment thickness or lithology or the presence of basement faults that channel circulating seawater. A thermal model that incorporates thermal conductivity variations along a profile from Canada Basin (thick sediment on mostly oceanic crust) to Alpha Ridge (thin sediment over thick magmatic units associated with the High Arctic Large Igneous Province) predicts heat flow lower than that observed on Alpha Ridge. This, along with other observations, implies that circulating fluids modulate conductive heat flow and contribute to high variability in the T-3 dataset. .

A phylogenomic supertree of birds

Released July 10, 2019 14:33 EST

2019, Diversity (11) 35

Rebecca T Kimball, Carl H Oliveros, Ning Wang, Noor D White, F. Keith Barker, Daniel J Field, Daniel T Ksepka, Terry Chesser, Robert G Moyle, Michael J Braun, Robb T Brumfield, Brant C Faircloth, Brian Tilston-Smith, Edward L Braun

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally-efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used this to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

Extent of the Last Glacial Maximum (Tioga) glaciation in Yosemite National Park and vicinity, California

Released July 10, 2019 12:07 EST

2019, Scientific Investigations Map 3414

Clyde Wahrhaftig, Greg M. Stock, Reba G. McCracken, Peri Sasnett, Andrew J. Cyr

Yosemite National Park, located in the central Sierra Nevada in California, is an icon of the U.S. National Park system. It is famous for its many spectacular geologic features, which include the towering cliffs and hanging waterfalls of Yosemite Valley and the rounded granite domes, deep blue lakes, and jagged peaks and spires of the high country. More subtle but just as spectacular are the vast areas of polished granite, linear scratches, and isolated boulders scattered across the landscape. All of these features owe their origin, at least in part, to glaciers. Glaciers originating at the crest of the Sierra Nevada flowed down preexisting river canyons numerous times throughout the Quaternary Period (the past 2.6 million years). Although the field evidence for past glaciations is necessarily incomplete, at least seven distinct glacial periods have been identified in the Sierra Nevada, spanning a minimum of 1.5 million years.

This map shows the extent of alpine icefields and associated valley glaciers in Yosemite National Park and vicinity during the most recent large glaciation, known as the Last Glacial Maximum, a globally recognized cold period characterized by low sea levels and the growth of ice sheets and mountain glaciers. In the Sierra Nevada, the Last Glacial Maximum glaciation is referred to as the Tioga glaciation. By virtue of being the most recent of the large Pleistocene glaciations, the evidence for the Tioga glaciation is abundant and relatively well preserved in the Yosemite landscape. The Tioga glaciation likely involved at least two, and perhaps as many as four, major glacial advances spanning the interval from approximately 27,000 to 15,000 years ago; the largest of these, representing the maximum ice extent shown on the map, occurred from approximately 21,000 to 18,000 years ago. Although it is possible that the various Tioga-age glaciers in the study area attained their maximum extents at slightly different times during the Last Glacial Maximum, for the purposes of this map we assume that they reached their maximum extents simultaneously. The maximum ice extent shown here may have occupied certain areas only briefly.

During the maximum extent of the Tioga glaciation, glaciers and ice fields covered most areas in and around Yosemite National Park above 2,700 meters elevation, having a profound impact on the Yosemite landscape. In addition to sculpting most of the granite monoliths for which the park is famous, glaciation also dictated the distribution of many geological, hydrological, and ecological features. Thus, the lasting effects of Tioga glaciation are still readily observable in Yosemite National Park today.

Bundle adjustment using space based triangulation method for improving the Landsat global ground reference

Released July 10, 2019 11:58 EST

2019, Remote Sensing (11)

James C. Storey, R. Rengarajan, Michael J. Choate

Michael Choate, editor(s)

There is an ever-increasing interest and need for accurate geo-registration of remotely sensed data products to a common global geometric reference. Although the geo-registration has improved significantly in the last decade, the lack of an accurate global ground reference dataset poses serious issues for data providers seeking to make geometrically stackable analysis ready data. The existing Global Land Survey 2000 (GLS2000) dataset derived from Landsat 7 images provide global coverage and can be used as a reference dataset, but its accuracy is much lower than what can be attained using the agile and precise pointing capability of the new spacecrafts. The improved position and pointing knowledge of the new spacecrafts such as Landsat 8 can be used to improve the accuracy of the existing global ground control points using a space based triangulation method. This paper discusses the theoretical basis, formulation, and application of the space based triangulation method at a continental scale to improve the accuracy of the GLS-derived ground control points.Our triangulation method involves adjusting the spacecraft position, velocity, attitude, attitude rate, and ground control point locations, iteratively, by linearizing the non-linear viewing geometry, such that the residual errors in the measured image points are minimized. The complexity of the numerical inversion and processing is dealt with in our approach by processing and eliminating the ground points one at a time. This helps to reduce the size of the normal matrix significantly, thereby making the triangulation of a continent-wide scale block feasible and efficient. One of the unique characteristics of our method is the use of a correlation model linking the attitude corrections between images of the same pass, which promotes consistency in the attitude corrections. We evaluated the performance of our triangulation method over the Australian continent using the Australian Geographic Reference Image (AGRI) dataset as a reference. Both a free adjustment, using only the pointing information of the Landsat 8 spacecraft, and a constrained adjustment, using the AGRI as external control were performed and the results compared. The Australian block’s horizontal accuracy improved from 15.4 m to 3.6 m with the use of AGRI controls, and from 15.4 m to 8.8 m without the use of AGRI controls.

First examination of diet items consumed by wild-caught black carp (Mylopharyngodon piceus) in the U.S.

Released July 10, 2019 10:28 EST

2019, The American Midland Naturalist (182) 89-108

Barry C. Poulton, Patrick Kroboth, George Aiken, Duane C. Chapman, J. Bailey, Stephen E. McMurray, John S. Faiman

Black carp (Mylopharyngodon piceus) were imported to the U.S. in the 1970s to control snails in aquaculture ponds and have since escaped from captivity. The increase in captures of wild fish has raised concerns of risk to native and imperiled unionid mussels given previous literature classified this species a molluscivore. We acquired black carp from commercial fishers and biologists, and examined digestive contents of 109 fish captured over 8 y from lentic and lotic habitats in the central and southern U.S.A. Digestive tract contents were preserved, and diet items inventoried. We identified 59 aquatic animal taxa (21 mollusks, 27 insects, and 11 other invertebrates) and various plant material including nuts and seeds; no fish were found. Approximately 45% of stomachs examined were empty or only contained flukes (Trematoda) that had infected mollusks before they were ingested. Nonempty stomachs contained snails (16.5%), bivalve mussels (22.8%), and insect larvae (net-spinning caddisflies, 15.6%; burrowing mayflies, 6.4%; and midges, 13.7%). Fish also consumed freshwater sponges (Porifera), moss animals (Bryozoa), crustaceans (Ostracoda and Decapoda), water mites (Acarina), and three worm phyla (Nematoda, Nemertea, Annelida). Seven taxa of unionid mussels were identified from shell fragments among the fish we examined, all of which are found in habitats with soft mud or sand/silt substrates. Diet of fish captured in lentic environments contained significantly higher richness than those captured in lotic environments. Individual black carp often contained large numbers of only one or two diet items that were assumed locally abundant and did not always crush the shells of mollusks. Most fish we examined consumed benthic prey, which supports the classification of black carp as a benthic foraging species. However, the presence of other aquatic taxa associated with pelagic or subsurface zones suggests black carp are opportunistic in their consumption of diet items and flexible in their feeding modes.

Safety in numbers: Cost-effective endangered species management for viable populations

Released July 09, 2019 14:32 EST

2019, Land Economics (95) 435-453

Pierce Donovan, Lucas S. Bair, Charles B. Yackulic, Michael R. Springborn

We develop a bioeconomic model to identify the cost-effective control of an invasive species (rain-bow trout) to achieve a population viability goal for an endangered species (humpback chub) in the Grand Canyon of the U.S. southwest. The population viability optimization problem is no-toriously difficult to solve due to a probabilistic restriction on joint outcomes (survival) over many periods. We develop a novel dynamic programming solution approach that is fast and forgoes the simulation method requirement of imposing structure on the policy function. We also investigate an adaptive management model that incorporates learning about uncertain bi-ological dynamics.

Predictive analysis using chemical-gene interaction networks consistent with observed endocrine activity and mutagenicity of U.S. streams

Released July 09, 2019 11:59 EST

2019, Environmental Science & Technology

Jason P. Berninger, David M. DeMarini, Sarah H. Warren, Jane Ellen Simmons, Vickie S. Wilson, Justin M. Conley, Mikayla D. Armstrong, Dana W. Kolpin, Kathryn Kuivila, Timothy J. Reilly, Kristin M. Romanok, Daniel L. Villeneuve, Paul M. Bradley, Luke R. Iwanowicz

In a recent U.S. Geological Survey/U.S. Environmental Protection Agency study assessing >700 organic compounds in 38 streams, in vitro assays indicated generally low estrogen, androgen, and glucocorticoid receptor activities, but identified 13 surface waters with 17β estradiol equivalent (E2Eq) activities greater than the 1 ng/L level of concern for feminization of male fish. Among the 36 samples assayed for mutagenicity in the Salmonella bioassay (reported here), 25% were considered mutagenic (statistically significant slope and at least a two-fold increase in revertants/plate). Endocrine and mutagenic activities of the water samples were well correlated with each other and with the total number and cumulative concentrations of detected chemical contaminants. To test the predictive utility of knowledgebase-leveraging approaches, site-specific predicted chemical-gene (pCGA) and predicted analogous pathway-linked (pPLA) association networks identified in the Comparative Toxicogenomics Database were compared with observed endocrine/mutagenic bioactivities. We evaluated pCGA/pPLA patterns among sites by cluster analysis and principal component analysis and grouped the pPLA into broad mode-of-action classes. Measured E2Eq and mutagenic activities correlated well with predicted pathways. The pPLA analysis also revealed correlations with signaling, metabolic, and regulatory groups, suggesting that other effects pathways may be associated with chemical contaminants in these waters and indicating the need for broader bioassay coverage to assess potential adverse impacts.

Hydrologic study at Farm Creek Marsh, Dorchester County, Maryland, from April 2015 to April 2016

Released July 09, 2019 11:50 EST

2019, Scientific Investigations Report 2019-5032

Charles W. Walker, Todd R. Lester, Christopher W. Nealen

In 2015, the U.S. Geological Survey began a 1-year hydrologic study to investigate the extent and cause of inundation at Farm Creek Marsh, in Dorchester County, Maryland. In combination with a tide and precipitation gage, a representative section of the marsh was instrumented with surface-water monitors and shallow groundwater piezometers to capture the spatial and temporal extent of inundation. In addition, water-quality data (major ions and nutrients) were collected to help discern the cause of inundation. Results indicate that during the year-long study, all sites were periodically inundated, ranging from a total of 108 days to the entire study period of 353 days. The depth of inundation was typically between 0 and 0.2 feet (ft) (above land surface), with the exception of large storm events. Less than 0.5 ft of elevation was the difference between a site being inundated during the entire study period of 353 days and a site being inundated for 36 consecutive days out of 108 total days of inundation during the study period. Water-quality data showed a large difference in pH between marsh surface water (6.1 to 6.9 standard pH units) and shallow groundwater (3.0 to 3.6 standard pH units), with differences also observed in concentrations of silica, iron, manganese, and potassium. Collectively, the combination of water-quality, hydrologic, and soils data indicate that inundation is caused by tide and storm events rather than groundwater discharge.

Examination of movements and survival of Pahranagat roundtail chub (Gila robusta jordani) in the Pahranagat River and adjacent waters, Nevada, 2014–18

Released July 08, 2019 14:43 EST

2019, Open-File Report 2019-1075

Barbara A. Martin, Brian S. Hayes, Alta C. Harris

Executive Summary

The Pahranagat roundtail chub (Gila robusta jordani; hereinafter “chub”) was federally listed as endangered in 1970 (U.S. Fish and Wildlife Service, 1970). In the decades following the listing, the chub has declined to extremely low numbers (Tuttle and others, 1990; Guadalupe, 2014). Loss of available habitat appears to be one of the main reasons for the decline of this species. Historically, the chub are assumed to have had approximately 30 kilometers (km) of habitat available to them, whereas currently they appear to primarily occupy 3.5 km of the Pahranagat River, up to 2.5 km of the Pahranagat Ditch, and a small portion of the Pahranagat Drain. Each year in mid-March, a gate at the top of the fish passage structure is closed to divert water down the Pahranagat Ditch, almost completely eliminating any flow into the Pahranagat Drain. The gate is usually removed in mid-October, allowing for flow to reoccur in the Pahranagat Drain. Due to the intermittent nature of the Pahranagat Drain, it is considered a sink for the species, and yearly salvage operations are conducted to remove chub from the Pahranagat Drain. The lower portion of the Pahranagat Ditch is also thought to be a sink for the species, due to high flows and limited structure potentially pushing the chub out of the system. Movements of passive-integrated-transponder (PIT) tagged chub indicate that adults and larger juveniles are not likely to be swept downstream to the point of exiting the system; however, the smaller juveniles and larvae are likely to be entrained in the Pahranagat Drain and possibly the lower portion of the Pahranagat Ditch. Only 2 of 64 PIT-tagged chub (3 percent) were observed to exit the system through the Pahranagat Ditch as they were last recorded on the Lower Ditch antenna. No PIT-tagged chub was observed exiting the system through the Pahranagat Drain.

Although capture location was a good predictor of where PIT tagged fish were primarily detected, fish were observed to meander throughout the available habitat. Chub captured and released in the Pahranagat River were detected more often in the upper portion of the Pahranagat River, whereas chub captured and released in the Pahranagat Ditch were more often detected in and near the Pahranagat Ditch. This suggests some degree of site fidelity. However, the two chub that were captured in the Pahranagat Drain and relocated into the middle portion of the Pahranagat River near the Between Bridges antenna were not able to get back to the closed off Pahranagat Drain (closed to fish passage from mid-March through mid-October), but were primarily detected in and near the Pahranagat Ditch. Movements from one end of the system to the other end of the system (3.5 km) could occur within a day and there were no observed seasonal location preferences for the chubs. However, there was more activity in the uppermost sites during fall and winter, presumedly associated with spawning. Furthermore, chub were found to be more active during the daylight hours in fall and winter verses spring and summer. During summer, chubs were the least active, especially during daylight hours.

Most of the fish tagged were estimated to be adults based on size; 84 percent of fish tagged in this study were greater than 100 millimeters (mm) total length (TL). One chub monitored during this study (139 mm TL when tagged) was observed for a total of 714 days following capture, indicating that chub can survive at least 3 years. Furthermore, two fish greater than 200 mm TL when tagged were detected for another 7 months after tagging, which supports life history descriptions in the Recovery Plan that states Pahranagat roundtail chub can reach 250 mm TL (U.S. Fish and Wildlife Service, 1998). In addition to natural mortality events, fish may die from extreme temperatures or other environmental stressors. None of the fish tagged in 2014 or 2015 were detected past August 31, 2016, which suggests that there may have been some external influence causing mortality of the few remaining fish from May 1, 2016, to August 31, 2016. Although habitat for chub has been limited for decades to a very small section of the Pahranagat River and the Pahranagat Ditch (U.S. Fish and Wildlife Service, 1998), this study suggests that recent declining numbers of chub are most likely due to mortality events and not due to the fish emigrating from the system through the Pahranagat Ditch or the Pahranagat Drain.

One Health: A perspective from wildlife and environmental health sectors

Released July 08, 2019 13:03 EST

2019, Scientific and Technical Review (38) 91-98

Jonathan M. Sleeman, Katherine L. D. Richgels, C. LeAnn White, C. Stephen

Loss of biodiversity, habitat fragmentation and pollution, and subsequent degradation of natural environments threaten the range of ecosystem services that support all life on this planet. These changes, among others, are also driving the emergence of infectious diseases, with negative health outcomes for humans, animals, and our shared environment. Historically, interventions aimed at human and agricultural health issues did not always integrate wildlife or environmental health as part of the solution, which has resulted in unintended consequences. One Health recognises the  interdependence of humans, animals and their shared environment, and provides a conceptual framework for developing interventions that optimise outcomes for human, animal and environmental health. However, there is a need to clearly articulate the core values, goals, and objectives of One Health for all relevant sectors in order to maximise synergies for communication, coordination, collaboration, and, ultimately, for joint actions on disease control and prevention. Application of systems and harm reduction approaches, focusing on the socio-economic and environmental determinants of health, and ensuring good governance and effective leadership will also maximise the opportunities to develop ‘win-win-win’ solutions to global health and environmental challenges. These solutions would help propel One Health forward to reach its full potential and truly optimise health outcomes for all.

Report from the Ice and Climate Evolution Science Analysis group (ICE-SAG)

Released July 08, 2019 11:25 EST

2019, Report

Than Putzig, Serina Diniega, Colin M. Dundas, Timothy N. Titus

This document is the final report of the Ice and Climate Evolution Science Analysis Group (ICESAG) that was formed by the Mars Exploration Program Analysis Group (MEPAG) as part of its preparations for the upcoming NASA Planetary Science Decadal Survey for 2023 through 2032 (see §1). Through telecons, one face-to-face meeting, and discussions with experts in relevant topics, ICE-SAG has identified high-priority science questions and key measurements that are needed to address them as well as the 2018 MEPAG Goals and the 2013-2022 NASA Planetary Science Decadal Survey goals [V&V, 2011] pertaining to ice1 and climate. Obtaining these measurements would yield dramatic improvements in our understanding of the climate history of Mars, which is critical to investigations of Martian geologic history and habitability and will also inform the potential of buried water ices as in situ resources for future human missions. In many ways, the Martian climate system serves as a laboratory for a broader understanding of planetary climate systems including the Earth’s, which is substantially more complex due to a denser atmosphere, a more active planetary interior, and interactions with oceans and abundant life, while operating under much more subtle orbital forcing. Thus, advancements in Martian climate science will have far-reaching impacts that extend to studies of the Earth and other planetary bodies.

Timber harvest alters mercury bioaccumulation and food web structure in headwater streams

Released July 06, 2019 16:18 EST

2019, Environmental Pollution (253) 636-645

James Willacker, Collin A. Eagles-Smith, Brandon M Kowalski, Robert J Danehy, Allyson K. Jackson, Evan M. Adams, David C. Evers, Chris S. Eckley, Michael T. Tate, David P. Krabbenhoft

Timber harvest has many effects on aquatic ecosystems, including changes in hydrological, biogeochemical, and ecological processes that can influence mercury (Hg) cycling. Although timber harvest’s influence on aqueous Hg transformation and transport are well studied, the effects on Hg bioaccumulation are not. We evaluated Hg bioaccumulation, biomagnification, and food web structure in 10 paired catchments that were either clear-cut in their entirety, clear-cut except for an 8-m wide riparian buffer, or left unharvested. Average mercury concentrations in aquatic biota from clear-cut catchments were 50% higher than in reference catchments and 165% higher than in catchments with a riparian buffer. Mercury concentrations in aquatic invertebrates and salamanders were not correlated with aqueous THg or MeHg concentrations, but rather treatment effects appeared to correspond with differences in the utilization of terrestrial and aquatic basal resources in the stream food webs. Carbon and nitrogen isotope data suggest that a diminished shredder niche in the clear-cut catchments contributed to lower basal resource diversity compared with the reference of buffered treatments, and that elevated Hg concentrations in the clear-cut catchments reflect an increased reliance on aquatic resources in clear-cut catchments. In contrast, catchments with riparian buffers had higher basal resource diversity than the reference catchments, indicative of more balanced utilization of terrestrial and aquatic resources. Further, following timber harvest THg concentrations in riparian songbirds were elevated, suggesting an influence of timber harvest on Hg export to riparian food webs. These data, coupled with comparisons of individual feeding guilds, indicate that changes in organic matter sources and associated effects on stream food web structure are important mechanisms by which timber harvest modifies Hg bioaccumulation in headwater streams and riparian consumers.

Lidar-based approaches for estimating solar insolation in heavily forested streams

Released July 05, 2019 14:21 EST

2019, Hydrology and Earth System Sciences (23) 2813-2822

Jeffrey J Richardson, Christian E. Torgersen, L Monika Moskal

Methods to quantify solar insolation in riparian landscapes are needed due to the importance of stream temperature to aquatic biota. We have tested three lidar predictors using two approaches developed for other applications of estimating solar insolation from airborne lidar using field data collected in a heavily forested narrow stream in western Oregon, USA. We show that a raster methodology based on the light penetration index (LPI) and a synthetic hemispherical photograph approach both accurately predict solar insolation, explaining more than 73 % of the variability observed in pyranometers placed in the stream channel. We apply the LPI-based model to predict solar insolation for an entire riparian system and demonstrate that no field-based calibration is necessary to produce an unbiased prediction of solar insolation using airborne lidar alone.

Long-term (1986–2015) crop water use characterization over the Upper Rio Grande Basin of United States and Mexico using Landsat-based evapotranspiration

Released July 04, 2019 10:36 EST

2019, Remote Sensing (11)

Gabriel Senay, Matthew (Contractor) Schauer, Naga Manohar (Contractor) Velpuri, Ramesh (Contractor) Singh, Stefanie (Contractor) Kagone, MacKenzie (Contractor) Friedrichs, Marcy Litvak, Kyle R. Douglas-Mankin

The evaluation of historical water use in the Upper Rio Grande Basin (URGB), United States and Mexico, using Landsat-derived actual evapotranspiration (ETa) from 1986 to 2015 is presented here as the first study of its kind to apply satellite observations to quantify long-term, basin-wide crop consumptive use in a large basin. The rich archive of Landsat imagery combined with the Operational Simplified Surface Energy Balance (SSEBop) model was used to estimate and map ETa across the basin and over irrigated fields for historical characterization of water-use dynamics. Monthly ETa estimates were evaluated using six eddy-covariance (EC) flux towers showing strong correspondence (r2 > 0.80) with reasonable error rates (root mean square error between 6 and 19 mm/month). Detailed spatiotemporal analysis using peak growing season (June–August) ETa over irrigated areas revealed declining regional crop water-use patterns throughout the basin, a trend reinforced through comparisons with gridded ETa from the Max Planck Institute (MPI). The interrelationships among seven agro-hydroclimatic variables (ETa, Normalized Difference Vegetation Index (NDVI), land surface temperature (LST), maximum air temperature (Ta), potential ET (ETo), precipitation, and runoff) are all summarized to support the assessment and context of historical water-use dynamics over 30 years in the URGB.

Integrative taxonomy reveals a new species of freshwater mussel, Potamilus streckersoni sp. nov. (Bivalvia: Unionidae): Implications for conservation and management

Released July 03, 2019 15:23 EST

2019, Systematics and Biodiversity (17) 331-348

Chase H. Smith, Nathan Johnson, Kentaro Inoue, Robert Doyle, Charles R. Randklev

Inaccurate systematics confound our ability to determine evolutionary processes that have led to the diversification of many taxa. The North American freshwater mussel tribe Lampsilini is one of the better-studied groups in Unionidae, however, many supraspecific relationships between lampsiline genera remain unresolved. Two genera previously hypothesized to be non-monophyletic that have been largely overlooked are Leptodea and Potamilus. We set out to resolve supraspecific relationships in Lampsilini and test the monophyly of Leptodea and Potamilus by integrating molecular, morphological, and life history data. Our molecular matrix consisted of four loci: cytochrome c oxidase subunit 1 (CO1), NADH dehydrogenase subunit 1 (ND1), internal transcribed spacer 1 (ITS1), and 28S ribosomal RNA. Secondly, we performed both traditional and Fourier shape morphometric analyses to evaluate morphological differences and finally, we compared our results with available life history data. Molecular data supported the paraphyly of both Leptodea and Potamilus, but nodal support was insufficient to make any conclusions regarding generic-level assignments at this time. In contrast, inference from our integrative taxonomic assessment depicts significant support for the recognition of a new species, Potamilus streckersoni sp. nov., the Brazos Heelsplitter. Our data show clear separation of three taxonomic entities in the P. ohiensis species complex: P. amphichaenus, P. ohiensis, and P. streckersoni sp. nov.; all molecularly, geographically, and morphologically diagnosable. Our findings have profound implications for unionid taxonomy and will aid stakeholders in establishing effective conservation and management strategies.http://www.zoobank.org/urn:lsid:zoobank.org:pub:502647C0-418B-4CC4-85A8-BD89FC3F674F

Cell-Based metabolomics for untargeted screening and prioritization of vertebrate-active stressors in streams across the United States

Released July 03, 2019 15:11 EST

2019, Environmental Science & Technology

Timothy W. Collette, Drew R. Ekman, Huajun Zhen, Ha Nguyen, Paul Bradley, Quincy Teng

The U.S. Geological Survey and the U.S. Environmental Protection Agency have assessed contaminants in 38 streams across the U.S., using an extensive suite of target-chemical analysis methods along with a variety of biological effects tools. Here we report zebrafish liver (ZFL) cell-culture based NMR metabolomic analysis of these split stream samples. We used this untargeted approach to evaluate the sites according to overall impact on the ZFL metabolome and found that neither the total number of organics detected at the sites, nor their cumulative concentrations, were good predictors of these impacts. Further, we used partial-least squares regression to compare ZFL endogenous metabolite profiles to values for 455 potential stressors (organics, inorganics, and physical properties) measured in these waters and found that the profiles covaried with at most 280 of the stressors, which were subsequently ranked into quartiles based on the strength of their covariance. While contaminants of emerging concern (CECs) were well represented in the top, most strongly, covarying quartile – suggesting considerable potential for eliciting biological responses at these sites – there was even higher representation of various well-characterized legacy contaminants (e.g., PCBs). These results emphasize the importance of complementing chemical analysis with untargeted bioassays to help focus regulatory efforts on the most significant ecosystem threats.

A comprehensive approach uncovers hidden diversity in freshwater mussels (Bivalvia: Unionidae) with the description of a novel species

Released July 02, 2019 15:11 EST

2019, Cladistics (Online First)

Kentaro Inoue, John L. Harris, Clint Robertson, Nathan Johnson, Charles R. Randklev

Major geological processes have shaped biogeographical patterns of riverine biota. The Edwards Plateau of central Texas, USA, exhibits unique aquatic communities and endemism, including several species of freshwater mussels. Lampsilis bracteata (Gould, 1855) is endemic to the Edwards Plateau region; however, its phylogenetic relationship with other species in the Gulf coastal rivers and Mississippi River basin is unknown. We evaluated phylogenetic relationships, shell morphologies and soft anatomy characters of L. bracteata and a closely related congener, Lampsilis hydiana (Lea, 1838) throughout their ranges. Our results showed the presence of an undescribed species: Lampsilis bergmannisp.n. Lampsilis bracteata and L. bergmanni sp.n. share similar shell morphologies and soft anatomy characters; however, they are genetically distinct. Geological processes, such as faulting and sea‐level changes during the Miocene to Pliocene, are likely to have facilitated diversification of Lampsilis species, resulting in isolation of L. bracteata on the Edwards Plateau and diversification between L. bergmanni sp.n. and L. hydiana. We conclude that L. bracteata range is restricted to the Colorado River basin, whereas L. bergmanni sp.n. occurs only in upstream reaches of the Guadalupe River basin. Conservation actions are warranted for both species due to their restricted distributions and potential anthropogenic threats.

Perspective: Developing flow policies to balance the water needs of humans and wetlands requires a landscape scale approach inclusive of future scenarios and multiple timescales

Released July 02, 2019 14:29 EST

2019, Wetlands 1-13

Brent Murry, Jared Bowden, Benjamin Branoff, Miguel Garcia-Bermudez, Beth Middleton, Jorge Ortiz-Zayas, Carla Restrepo, Adam Terando

Maintenance of the natural flow regime is essential for continued wetland integrity; however, the flow regime is greatly influenced by both natural and anthropogenic forces. Wetlands may be particularly susceptible to altered flow regimes as they are directly impacted by water flows at a variety of time scales. In Puerto Rico, contemporary water management is decreasing freshwater recharge to wetlands and contributes to the salinization of important coastal wetlands as sea levels rise. Further, downscaled climate models predict an increase in drought frequency, intensity, and duration by mid-century. Conflicts over water allocation seem imminent between human and ecological needs. Current minimum flow policies are insufficient given the complexities of ecosystem processes and the changes in precipitation patterns and sea level rise that are expected in the future. Improved flow policies need to be established that reflect the functional relationships between specific representative ecological resources and components of the natural flow regime across all relevant time scales. Similarly, flow policies need to be developed within a landscape scale to implicitly address the socio-ecological trade-offs as well as the complexities of water management. Multi-disciplinary collaborations will be essential for increasing our resiliency to anticipated future changes.

Hydrologic site assessment for passive treatment of groundwater nitrogen with permeable reactive barriers, Cape Cod, Massachusetts

Released July 02, 2019 14:15 EST

2019, Scientific Investigations Report 2019-5047

Jeffrey R. Barbaro, Marcel Belaval, Danna B. Truslow, Denis R. LeBlanc, Thomas C. Cambareri, Scott C. Michaud

Wastewater disposal associated with rapid population growth and development on Cape Cod, Massachusetts, during the past several decades has resulted in widespread contamination of groundwater with nitrogen. As a result, water quality in many of the streams, lakes, and coastal embayments on Cape Cod is impaired by excess nitrogen. To reduce nitrogen loads to these impaired water bodies, watershed-based planning is currently [2019] underway following a regional strategy, the section 208 areawide water-quality management plan update for Cape Cod. In the updated plan, traditional (sewering) and alternative wastewater management options are under consideration for restoring water quality in impaired surface-water bodies. Permeable reactive barriers, which are reactive zones emplaced below the water table for passive treatment of groundwater contaminants, are one of the alternatives being considered by Cape Cod towns as a potentially cost-effective technology for the removal of nitrogen from groundwater. However, the effectiveness of permeable reactive barriers depends on local conditions, and site-specific hydrologic and water-quality data are needed to inform the decision to install a permeable reactive barrier in a given location. These data are not available in most locations on Cape Cod; consequently, site assessments are needed before selecting this treatment option.

To address this need, the U.S. Environmental Protection Agency, U.S. Geological Survey, and Cape Cod Commission formed a technical team in 2015 to develop and evaluate a hydrologic site-assessment approach for permeable reactive barrier installation. The approach developed by the technical team includes a preliminary regional assessment followed by a phased onsite investigation. The approach was intended to provide the hydrologic data needed to make informed decisions on site suitability and to support installation and monitoring should the site be deemed appropriate for a permeable reactive barrier. The factors that were evaluated to characterize local hydrologic conditions and inform site selection included groundwater flow directions and rates, depth to the water table, hydraulic conductivity and degree of heterogeneity of the aquifer, spatial distribution and concentration of nitrate and oxidation-reduction-sensitive constituents, thickness and depth of the treatment zone, distance to downgradient water bodies, and access for drilling and permeable reactive barrier installation. The approach was demonstrated on Cape Cod by conducting a preliminary assessment of 27 sites, from which 5 sites were selected for onsite investigations. Results indicated that the site-assessment approach was successful for screening sites and characterizing the geologic, hydrologic, and water-quality conditions at the sites selected for onsite investigations. Overall, the phased assessment evaluated in this study provided an efficient means of obtaining the hydrologic information needed to determine if a site was suitable for permeable reactive barrier installation on Cape Cod for the passive treatment of nitrogen in groundwater.

Sharp savanna-forest transitions in the Midwest followed environmental gradients but are absent from the modern landscape

Released July 01, 2019 16:12 EST

2019, The American Midland Naturalist (180) 1-17

Caitlin M. Broderick, Kelly A Heilman, Tamatha Patterson, Jody A Peters, Jason S. McLachlan

Historically, closed eastern forests transitioned into open savannas and prairies in the US Midwest, but this transition is poorly understood. To investigate the eastern boundary of the prairie-forest ecotone, we conducted a case study of historic and modern vegetation patterns of the Yellow River watershed in northwest Indiana. Historic vegetation came from the Public Land Survey notes collected in the early 1800s, whereas modern vegetation came from the Forest Inventory Analysis and USGS National Land Cover Database. We mapped historical survey vegetation data using GIS to reconstruct the region’s past and current forest composition and structure. We also mapped climate, topography, and soil composition across the watershed to investigate the relationship between historic vegetation and environmental gradients. We found a sharp transition in the presettlement forest structure and composition, with dense deciduous forests in the eastern portion of our study area and open oak savannas in the west. The savanna ecosystem dominated in sandy well-drained soils and was at a slightly lower elevation than the adjacent closed forest. Modest environmental changes accompanied major vegetation changes in the past, which might suggest fire and hydrological patterns helped maintain the sharp ecotone. By contrast, the modern forest shows no difference in tree density and composition across the watershed, which is consistent with major land use and hydrology changes in the watershed since settlement. On the modern landscape, land that was historically closed forest now has higher agricultural productivity compared to land that was historically savanna, whereas the historic savanna currently supports more mesic forest. These results suggest the environmental gradient continues to subtly shape the landscape. Though land use change has largely removed the closed mixed hardwood forests and oak savannas from this area, a better understanding of the historic vegetation and the conditions that supported it can help inform land management and restoration, as well as reveal ecological processes that drive vegetation transitions.

Differentiating anthropogenic and natural sources of uranium by geochemical fingerprinting of groundwater at the Homestake Uranium Mill, Milan, New Mexico, USA

Released June 29, 2019 07:37 EST

2019, Environmental Earth Sciences (78)

Johanna Blake, Philip Harte, Kent Becher

A multiparameter geochemical-isotopic fingerprinting approach was used to differentiate natural and anthropogenic signatures of uranium contamination near the Homestake uranium mill site (Site), near Milan, New Mexico, USA. The Site consists of two tailings piles from milling operations and groundwater contamination from these tailings have been noted. The Site lies within the lower San Mateo Creek Basin with multiple regional sources of U contamination from mining and mill operations and is underlain by a heterogeneous alluvial aquifer, which is underlain by basement rock of the Chinle Group and the lowermost San Andres-Glorieta aquifer. To help decipher signatures, several statistical approaches were used including PCA, NMDS, and cluster analysis. Trilinear piper diagrams indicate two end member water types at the Site, sulfate-Na-K and sulfate-Ca. Natural alluvial aquifer groundwater in this area, relatively unaffected by mining or milling, appears to be more dominated by bicarbonate than sulfate and the deeper San Andres-Glorieta aquifer that has a mixture of sulfate and bicarbonate. Uranium concentrations from the Site fall into three broad categories, less than the drinking water standard of 30 µg/L (n=3), from 30 to 100 µg/L (n=9) and greater than 100 µg/L (n=8). Component loadings in a principal component analysis are highest for uranium isotopes, 228Ra, gross alpha-beta, molybdenum, chloride, uranium, and sodium, which affect the similarities or differences among wells sampled. Results suggest that several alluvial wells upgradient from the Site have anthropogenic fingerprints from regional sources related to upgradient mining. Wells with higher uranium concentrations have uranium activity ratios close to 1, which is indicative of mining or milling signatures. These same wells have elevated radon activities. This information can be used to inform Site managers on the source of water related to uranium at the Site and provide an approach for geochemical fingerprinting.

Groundwater quality and hydrology with emphasis on selenium mobilization and transport in the Lower Gunnison River Basin, Colorado, 2012–16

Released June 28, 2019 13:00 EST

2019, Scientific Investigations Report 2019-5029

Judith C. Thomas, Peter B. McMahon, L. R. Arnold

Dissolved selenium is a contaminant of concern in the lower Gunnison River Basin, Colorado. Selenium is naturally present in the Cretaceous Mancos Shale and is leached to groundwater and surface water by irrigation. The groundwater on the east side of the Uncompahgre River in Delta and Montrose Counties is one of the primary sources of selenium concentration and load to surface water in the lower Gunnison River Basin. Although little information about the contribution of groundwater to surface water has been historically available, groundwater has often been implicated as an appreciable source of selenium to surface water. From 2012 to 2016, the U.S. Geological Survey, in cooperation with the Bureau of Reclamation, the Colorado Water Conservation Board, and the Gunnison Basin Selenium Management Program, established a 30-well groundwater-monitoring network on irrigated land to characterize the hydrology and groundwater quality of the shallow groundwater system on the east side of the Uncompahgre River in the lower Gunnison River Basin. The installation of the 30-well network and the data collected allowed for the development of a conceptual model of selenium mobilization and transport in the shallow groundwater system. Monitoring wells were completed in surficial deposits and in weathered Mancos Shale, which generally exhibited unconfined and confined conditions, respectively. Groundwater-quality monitoring provides information on the distribution of selenium and the geochemical processes controlling selenium concentrations in shallow groundwater. Monitoring wells were sampled between August 2013 and March 2015 to understand groundwater quality, seasonality, sources of recharge, and groundwater age. Concentrations of dissolved selenium ranged from below the limit of detection to 4,100 micrograms per liter (µg/L), with a median concentration of 14 µg/L. Concentrations showed a high degree of spatial variability and no seasonal difference. Similarly, no seasonal pattern was observed in specific conductance values of groundwater despite the considerably lower specific conductance value of irrigation water.

Reduction-oxidation processes are important controls on selenium mobility. Nitrate derived from geologic material was a primary control on reduction-oxidation conditions in groundwater and inhibited selenium reduction to less mobile forms. Nitrate was reduced by denitrification in groundwater, but it was not reduced to the extent necessary to allow for selenium reduction. Groundwater ages were determined for groundwater samples from eight wells and ranged from 6 to 20 years old. Isotopic data indicate groundwater was recharged by irrigation water; no information collected supported an older, deeper source of recharge to the shallow groundwater system. Data on water level in all wells showed response to irrigation practices, but the response was delayed in some wells, which may be an indication of distance from recharge source.

Effects of experimental removal of Barred Owls on population Demography of Northern Spotted Owls in Washington and Oregon—2018 Progress Report

Released June 28, 2019 10:34 EST

2019, Open-File Report 2019-1074

J. David Wiens, Katie M. Dugger, Damon B. Lesmeister, Krista E. Dilione, David C. Simon

Populations of Northern Spotted Owls (Strix occidentalis caurina; herineafter referred to as Spotted Owl) have declined throughout the subspecies’ geographic range. Evidence indicates that competition with invading Barred Owls (S. varia) has contributed significantly to those declines. A pilot study in California showed that removal of Barred Owls coupled with conservation of suitable habitat conditions can slow or even reverse population declines of Spotted Owls. It is unknown, however, whether similar results can be obtained in areas with different forest conditions, greater densities of Barred Owls, and fewer remaining Spotted Owls. We initiated a before-after-control-impact (BACI) experiment at three study areas in Oregon and Washington to determine if removal of Barred Owls can improve population trends of Spotted Owls. This report describes research accomplishments and initial results from the first 3.5 years of the study (March 2015–August 2018).

Improving pressure-limited CO2 storage capacity in saline formations by means of brine extraction

Released June 28, 2019 09:44 EST

2019, International Journal of Greenhouse Gas Control (88) 299-310

Hossein Jahediesfanjani, Steven T. Anderson, Peter D. Warwick

The carbon dioxide (CO2) storage capacity of saline formations may be constrained by reservoir pressure limitations. Brine extraction could be necessary to increase the CO2 storage capacity of a given formation, manage the extent of the underground CO2 plume and induced pressure front, and control the migration direction. To estimate the additional CO2 storage capacity of a saline formation that can be made accessible by extraction of in-situ brines, a three-dimensional (3D) generic cubic cell containing one CO2 injector in the middle surrounded by four brine extractors at each corner of the cell was assumed. A series of Tough2-ECO2N reservoir simulations were constructed with varying reservoir properties and run. Based on a series of scenarios, a mechanism was developed and demonstrated that resulted in derivation of a function to provide estimates of the ratio of total CO2 injection over the brine extraction rate for a given scenario. We selected multiple saline formations in U.S. basins and evaluated the potential to increase the combined dynamic CO2 storage capacity of the selected saline formations to over 1000 million metric tonnes per year (Mt/yr) of CO2 for 100 years by means of brine extraction. Such storage capacities may be adequate to accommodate the CO2 injection rates suggested for the United States under a “beyond two-degree Celsius scenario” (B2DS) that has been proposed to maintain global temperature rise to less than 2°C above pre-industrial reported levels. The results suggest that B2DS goals could be achieved with a volume ratio of brine extraction to CO2injection as low as 1:4, which is far lower than the ratios that have been commonly assumed in the literature.

Optimization of salt marsh management at the Chincoteague National Wildlife Refuge, Virginia, through use of structured decision making

Released June 28, 2019 08:30 EST

2019, Open-File Report 2019-1056

Hilary A. Neckles, James E. Lyons, Jessica L. Nagel, Susan C. Adamowicz, Toni Mikula, Kevin S. Holcomb

Structured decision making is a systematic, transparent process for improving the quality of complex decisions by identifying measurable management objectives and feasible management actions; predicting the potential consequences of management actions relative to the stated objectives; and selecting a course of action that maximizes the total benefit achieved and balances tradeoffs among objectives. The U.S. Geological Survey, in cooperation with the U.S. Fish and Wildlife Service, applied an existing, regional framework for structured decision making to develop a prototype tool for optimizing salt marsh management decisions at the Chincoteague National Wildlife Refuge in Virginia. Refuge biologists, refuge managers, and research scientists identified multiple potential management actions to improve the ecological integrity of 12 salt marsh management units within the refuge and estimated the outcomes of each action in terms of performance metrics associated with each management objective. Value functions previously developed at the regional level were used to transform metric scores to a common utility scale, and utilities were summed to produce a single score representing the total management benefit that would be accrued from each potential management action. Constrained optimization was used to identify the set of management actions, one per salt marsh management unit, that would maximize total management benefits at different cost constraints at the refuge scale. Results indicated that, for the objectives and actions considered here, total management benefits may increase consistently up to approximately $2.5 million, but that further expenditures may yield diminishing return on investment. For multiple salt marsh management units, a scenario incorporating managing grazing practices within the marsh was selected to maximize benefits while constraining total costs for the refuge at less than $2.5 million. Thin-layer deposition was predicted to increase the total management benefit substantially, but at considerable total costs ($2.5 million to $83 million). The prototype presented here provides a framework for decision making at the Chincoteague National Wildlife Refuge that can be updated as new data and information become available. Insights from this process may also be useful to inform future habitat management planning at the refuge.

Capacity and area of Grand Lake O’ the Cherokees, northeastern Oklahoma, 2009

Released June 27, 2019 19:35 EST

2019, Scientific Investigations Report 2019-5040

Shelby L. Hunter, Laura G. Labriola

In February 2017, the Grand River Dam Authority filed to relicense the Pensacola Hydroelectric Project with the Federal Energy Regulatory Commission. The predominant feature of the Pensacola Hydroelectric Project is Pensacola Dam, which impounds Grand Lake O’ the Cherokees (locally called Grand Lake) in northeastern Oklahoma. Identification of information gaps and assessment of project effects on stakeholders are central aspects of the Federal Energy Regulatory Commission relicensing process. Due to the natural changes to the reservoir over time, new capacity and area tables are needed periodically. The most recent complete capacity and area table was produced in 1940. Capacity and area tables identify the relations between the elevation of the water surface and the volume of water that can be impounded at each water surface elevation. This report (1) presents an updated capacity and area table for Grand Lake O’ the Cherokees for 2009, (2) describes the methods used to calculate the updated capacity and area values presented in the table, and (3) compares the updated capacity table to historical capacity tables produced from a survey in 1940 and from a hydrographic survey of the lake by the Oklahoma Water Resources Board in 2009.

The new capacity values computed for Grand Lake O’ the Cherokees indicate that capacity at conservation pool elevation has decreased about 157,000 acre-feet or 10 percent since 1940 and capacity at top of dam elevation has decreased about 200,000 acre-feet or 8 percent since 1940. This difference in the capacities could be attributed to the advancements of technologies; the techniques used for surveying lakes have changed from the 1940 survey to the 2009 survey. Another possible reason for loss in capacity could be as time progresses, lakes like Grand Lake O’ the Cherokees slowly impound sediment carried by the rivers that feed into the lakes, thus diminishing the amount of water that the lake holds. The most recent survey used measured water depths and Global Position System collected electronically, but the methods used to collect data in 1940 are unknown. Due to the advancement of technology, the 2009 survey is likely more precise than the 1940 survey.

Assessing potential effects of highway and urban runoff on receiving streams in total maximum daily load watersheds in Oregon using the stochastic empirical loading and dilution model

Released June 27, 2019 18:19 EST

2019, Scientific Investigations Report 2019-5053

Adam J. Stonewall, Gregory E. Granato, Kira M. Glover-Cutter

The Stochastic Empirical Loading and Dilution Model (SELDM) was developed by the U.S. Geological Survey (USGS) in cooperation with the Federal Highway Administration to simulate stormwater quality. To assess the effects of runoff, SELDM uses a stochastic mass-balance approach to estimate combinations of pre-storm streamflow, stormflow, highway runoff, event mean concentrations (EMCs) and stormwater constituent loads from a site of interest. In addition, SELDM can be used to assess the effects of stormwater Best Management Practices (BMPs), which are designed to mitigate the adverse effects of runoff into a waterbody. 

Adverse effects of stormwater on receiving waters are one of the greatest unsolved water-quality problems Nationwide. State DOTs, municipalities, Federal facilities, and private property owners who manage impervious surfaces need information about the potential magnitude of their contributions and the potential effectiveness of methods to mitigate the adverse effects of runoff. Because the efficacy of at-site controls are limited, information about the potential effectiveness of alternative strategies is needed. 

The USGS, in cooperation with the Oregon Department of Transportation (ODOT), conducted a study to research methods in which SELDM can be used to enhance the efficiency of ODOT’s stormwater program, support the development of a stormwater banking program, and meet environmental goals. Results can be used to develop a strategic, systems-level approach to stormwater management by considering entire watersheds instead of individual road crossings. Two watersheds, Bear Creek and Mill Creek, in western Oregon were selected for analysis. Within each watershed, seven road crossings were selected for demonstrating the utility of SELDM in nested basins.

Precipitation statistics, pre-storm streamflow, runoff coefficients, and hydrograph recession factors were calculated for each location and used in SELDM to simulate flow, water-quality concentrations, and constituent loads in the upstream basin, from the highway (or developed area), and downstream from the road crossing. Three water-quality constituents were selected for modeling: suspended-sediment concentration (SSC), total phosphorus (TP), and total copper (TCu). Using water-quality transport curves, the relations between streamflow and SSC and between streamflow and TP were simulated. Concentrations of TCu were simulated by configuring a linear relation between SSC and TCu. A generic BMP was simulated using the median treatment statistics for flow reductions, hydrograph extensions, concentration reductions, and minimum irreducible concentrations from nine BMP categories with data from the 2012 International BMP database. 

Five simulation scenarios were modeled for demonstrative purposes. These simulations were used to evaluate potential effects of different watershed properties, water-quality inputs, and stormwater mitigation measures. Instream EMCs were compared to hypothetical water-quality criteria for suspended sediment, total phosphorus, and total copper to demonstrate the concept of water-quality risk analysis. For all five scenarios, it was assumed that highway runoff concentrations were independent of location or average annual daily traffic. These five scenarios are as follows:
• Simulation Scenario 1—Natural Conditions (hereafter Simulation Scenario 1) represents conditions in an undeveloped watershed. This scenario demonstrates that the strategic placement of a hypothetical road crossing within a watershed could be used to avoid exceeding water-quality standards of TP and SSC, but that no location choice results in meeting TCu standards. Implementation of BMP had the most pronounced effects on downstream water-quality constituent EMCs at road crossings with the highest ratio of highway catchment area to upstream drainage area, but the largest effect of BMP treatment on mean annual load is based on highway catchment area alone.

• Simulation Scenario 2—Current Conditions (hereafter Simulation Scenario 2) represents current watershed conditions, where all developed area upstream from the road crossing was modeled as a highway and combined with the undeveloped part of the upstream drainage area (scenario 2A) and where the output from scenario 2A is used for the upstream area (developed area and the undeveloped area), and where the road crossing  is added as usual (scenario 2B). Scenario 2 results indicate that attaining water-quality standards is more difficult with upstream developed areas. Specific road-crossing sites can be selected to achieve the fewest water-quality exceedances per year, but water-quality targets are not met without BMP implementation, and in some instances are not achievable even with BMP implementation. Results from this scenario also serve to quantify the upper limit of constituent reduction if funding were available to implement BMPs to large areas of development, and to quantify how much area would need BMP implementation to achieve water-quality targets. 

• Simulation Scenario 3—Alternative Road Layouts (hereafter Simulation Scenario 3) was designed to assess the sensitivity of SELDM to various road layouts. In this scenario, different highway configurations were superimposed at one road crossing. Results indicate that downstream waterquality constituent EMCs did not exhibit much variation, but annual water-quality constituent loads varied considerably.
• Simulation Scenario 4—Varying Road Width (hereafter Simulation Scenario 4) was designed to assess the sensitivity of SELDM to road width. Similar to scenario 3, the results indicate little variation in downstream water-quality constituent EMCs, but annual water-quality constituent loads increased in proportion to road width.
• Simulation scenario 5—Changes to Impervious Area (hereafter Simulation Scenario 5) was designed to investigate the effects of changing amounts of imperviousness upstream from the road crossing.  Results indicate that the downstream water-quality constituent EMCs are highly correlated with the percentage of impervious area upstream.

Sand Creek characterization study for Oncorhynchus clarkii virginalis (Rio Grande Cutthroat Trout), Great Sand Dunes National Park and Preserve, Colorado

Released June 27, 2019 15:40 EST

2019, Scientific Investigations Report 2019-5061

Ben N. Mcgee, Andrew S. Todd, Kevin K. Terry

The Oncorhynchus clarkii virginalis (Rio Grande cutthroat trout, RGCT) has undergone extensive declines in distribution and population. The RGCT is the southernmost distributed subspecies of cutthroat trout. Native to the Rio Grande Basin in Colorado and New Mexico, the subspecies is also found in the headwaters of the Pecos River and Canadian River basins in New Mexico. Currently, RGCT populations represent approximately 12 percent of the historic distribution. There are many factors that have contributed to the decline of the RGCT including small population sizes; hybridization with non-native salmonids; competition with non-native salmonids; angling; and loss of habitat resulting from wildfire, stream drying, disease, increased water temperatures; and poor land management.

The eastern side of Colorado’s Rio Grande Basin is also home to Great Sand Dunes National Park and Preserve and the Sand Creek watershed. This study was designed to (1) characterize current physical and biological conditions of waterbodies within the Sand Creek watershed, from headwaters to lower terminus near the dune field; (2) characterize the spatial extent of existing fisheries within the Sand Creek watershed to inform the scope of potential future reclamation efforts; and (3) evaluate key limiting factors for a future native RGCT reintroduction.

Bathymetric profiles were completed for two lakes within the upper Sand Creek drainage to characterize the physical geometry of each lake and to estimate the total lake volume required for future piscicide treatment and (or) fish removal efforts. Physical and biological conditions evaluated included stream water temperature and intermittency, discharge, and the genetics and existing fish community distribution and composition within the Sand Creek watershed were key components of this study. A baseline established the geographic extent and biological constraints factored into future piscicide treatment planning and native trout reintroduction efforts.

As a result of this work, the Sand Creek watershed can be broken up into several distinct categories: Lakes that are good candidates for reclamation and reintroduction of RGCT, lakes that are poor candidates for reclamation, streams that currently have fish and are good candidates for reclamation and reintroduction, streams that currently lack fish and may be good candidates for introduction of RGCT, and streams that currently lack fish and are not good candidates for introduction of RGCT. This characterization study report is intended to inform State and Federal managers of the likelihood that the Sand Creek watershed can support a sustainable population of RGCT should they be reintroduced.

Hydrocarbons in upland groundwater, Marcellus Shale Region, Northeastern Pennsylvania and Southern New York, USA

Released June 27, 2019 14:57 EST

2019, Environmental Science & Technology ( 53) 8027-8035

Peter B. McMahon, Bruce D. Lindsey, Matthew D. Conlon, Andrew G. Hunt, Kenneth Belitz, Bryant Jurgens, Brian Varela

Water samples from 50 domestic wells located <1 km (proximal) and >1 km (distal) from shale-gas wells in upland areas of the Marcellus Shale region were analyzed for chemical, isotopic, and groundwater-age tracers. Uplands were targeted because natural mixing with brine and hydrocarbons from deep formations is less common in those areas compared to valleys. CH4-isotope, predrill CH4-concentration, and other data indicate that one proximal sample (5% of proximal samples) contains thermogenic CH4 (2.6 mg/L) from a relatively shallow source (Catskill/Lock Haven Formations) that appears to have been mobilized by shale-gas production activities. Another proximal sample contains five other volatile hydrocarbons (0.03–0.4 μg/L), including benzene, more hydrocarbons than in any other sample. Modeled groundwater-age distributions, calibrated to 3H, SF6, and 14C concentrations, indicate that water in that sample recharged prior to shale-gas development, suggesting that land-surface releases associated with shale-gas production were not the source of those hydrocarbons, although subsurface leakage from a nearby gas well directly into the groundwater cannot be ruled out. Age distributions in the samples span ∼20 to >10000 years and have implications for relating occurrences of hydrocarbons in groundwater to land-surface releases associated with recent shale-gas production and for the time required to flush contaminants from the system.

Morphology and genesis of giant seafloor depressions on the southeasterncontinental shelf of the Korean Peninsula

Released June 27, 2019 14:31 EST

2019, Marine Geology (415)

Deniz Cukur, Gee-Soo Kong, Jong-Hwa Chun, Moo-Hee Kang, In-Kwon Um, Taekhyun Kwon, Samuel Johnson, Kyong-O Kim

We identify and describe five giant seafloor depressions from the southeastern continental shelf of the Korean Peninsula using multibeam bathymetry, sub-bottom profiler, and multi-channel seismic reflection data, supplemented by piston cores. Multibeam bathymetry data from the shelf show four crescent-shaped depressions (SD1 to SD4) and one near-circular depression (SD5) within a group of NW-SE trending depressions, the largest covering an area of about 7 km2 on the seafloor. The depressions reach up to ~4.5 km in width and ~2 km in length and have asymmetric cross-sections. Some have depths as large as 40 m below the surrounding seafloor with walls as steep as 45°. The depressions are confined to water depths between 130 and 170 m and bounded on the north by a large submarine channel that was plausibly formed by fluvial or tidal processes during the Last Glacial Maximum (LGM) sea-level lowstand. Multi-channel seismic and sub-bottom profiler data reveal truncated depression walls and the presence of sediment drift deposits within the depressions, indicating that both erosion and deposition are active processes. Flaser and lenticular bedding in the cored drift deposits along with variable grain size (ranging between ~2.6 phi and ~4.3 phi) are diagnostic features of the bottom currents influenced by tidal forces. Depressions SD1 to SD4 lack evidence of fluid or gas escape. In contrast, many features of depression SD5 are characteristic of gas escapes and blowouts, including acoustic anomalies, a 20-m-high carbonate mound or carbonate-encrusted mound, and mud dikes and mud patches in cores. Based on the SD5 example, we think it is likely that the other crescent-shaped seafloor depressions formed originally as pockmarks by gas/fluid venting, and have since become inactive. The pockmarks represent zones of weakened sediment that were eroded, expanded, and merged by bottom currents to form larger seafloor depressions. Modern currents are strong enough to transport shelf sediments, and these currents were probably much stronger at lower sea levels when the Korea Strait was a more restricted passage between the East China Sea and East Sea.

Spatial conservation planning under uncertainty: adapting to climate change risks using modern portfolio theory

Released June 27, 2019 12:47 EST

2019, Ecological Applications

Mitchell Eaton, Simeon Yurek, Zulqarnain Haider, Julien Martin, Fred Johnson, Bradley J Udell, Hadi Charkhgard, Changhyun Kwon

Climate change and urban growth impact habitats, species, and ecosystem services. To buffer against global change, an established adaptation strategy is designing protected areas to increase representation and complementarity of biodiversity features. Uncertainty regarding the scale and magnitude of landscape change complicates reserve planning and exposes decision makers to risk of failing to meet conservation goals. Conservation planning tends to treat risk as an absolute measure, ignoring the context of the management problem and risk preferences of stakeholders. Application to conservation of risk management theory emphasizes diversification of portfolio of assets, with the goal of reducing the impact of system volatility on investment return. We use principles of Modern Portfolio Theory (MPT), which quantifies risk as the variance and correlation among assets, to formalize diversification as an explicit strategy for managing risk in climate‐driven reserve design. We extend MPT to specify a framework that evaluates multiple conservation objectives, allows decision makers to balance management benefits and risk when preferences are contested or unknown, and includes additional decision options such as parcel divestment when evaluating candidate reserve designs. We apply an efficient search algorithm that optimizes portfolio design for large conservation problems and a game theoretic approach to evaluate portfolio tradeoffs that satisfy decision makers with divergent benefit and risk tolerances, or when a single decision maker cannot resolve their own preferences. Evaluating several risk profiles for a case study in South Carolina, our results suggest that a reserve design may be somewhat robust to differences in risk attitude but that budgets will likely be important determinants of conservation planning strategies, particularly when divestment is considered a viable alternative. We identify a possible fiscal threshold where adequate resources allow protecting a sufficiently diverse portfolio of habitats such that the risk of failing to achieve conservation objectives is considerably lower. For a range of sea‐level rise projections, conversion of habitat to open water (14‐180%) and wetland loss (1‐7%) are unable to be compensated under the current protected network. In contrast, optimal reserve design outcomes are predicted to ameliorate expected losses relative to current and future habitat protected under the existing conservation estate.

A novel host-adapted strain of Salmonella Typhimurium causes disease in olive ridley turtles (Lepidochelys olivacea) in the Pacific.

Released June 27, 2019 12:02 EST

2019, Scientific Reports (9)

Thierry M. Work, Julie Dagenais, Brian A. Stacy, Jason T. Ladner, Jeffrey M. Lorch, George H. Balazs, Elias Barquero-Calvo, Brenda M. Berlowski-Zier, Renee Breeden, Natalia Corrales-Gómez, Rocio Gonzalez-Barrientos, Heather Harris, Gabriela Hernández-Mora, Angel Herrera-Ulloa, Shoreh Hesami, T. Todd Jones, Juan Alberto Morales, Terry M. Norton, Robert Rameyer, Daniel Taylor, Thomas B. Waltzek

Salmonella spp. are frequently shed by wildlife including turtles, but S. enterica subsp. enterica serovar Typhimurium or lesions associated with Salmonella are rare in turtles. Between 1996 and 2016, we necropsied 127 apparently healthy pelagic olive ridley turtles (Lepidochelys olivacea) that died from drowning bycatch in fisheries and 44 live or freshly dead stranded turtles from the west coast of North and Central America and Hawaii. Seven % (9/127) of pelagic and 47% (21/44) of stranded turtles had renal granulomas associated with S. Typhimurium. Stranded animals were 12 times more likely than pelagic animals to have Salmonella-induced nephritis suggesting that Salmonella may have been a contributing cause of stranding. S. Typhimurium was the only Salmonella serovar detected in L. olivacea, and phylogenetic analysis from whole genome sequencing showed that the isolates from L. olivacea formed a single clade distinct from other S. Typhimurium. Molecular clock analysis revealed that this novel clade may have originated as recently as a few decades ago. The phylogenetic lineage leading to this group is enriched for non-synonymous changes within the genomic area of Salmonella pathogenicity island 1 suggesting that these genes are important for host adaptation.

Flood-inundation maps for the Iowa River at the Meskwaki Settlement in Iowa, 2019

Released June 27, 2019 11:30 EST

2019, Scientific Investigations Report 2019-5050

Charles V. Cigrand

Digital flood-inundation maps for a 9.3-mile reach of the Iowa River along the Meskwaki Settlement, Iowa, were created by the U.S. Geological Survey (USGS) in cooperation with the Sac and Fox Tribe of the Mississippi in Iowa. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science website at https://water.usgs.gov/osw/flood_inundation/, depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage 05451770 on the Iowa River at County Highway E49 near Tama, Iowa. Near-real-time stages at this streamgage may be obtained on the internet from the USGS National Water Information System at https://waterdata.usgs.gov/ or the National Weather Service (NWS) Advanced Hydrologic Prediction Service  at https://water.weather.gov/ahps/, which also forecasts flood hydrographs at this site.

Flood profiles were computed for the stream reach by means of a calibrated one-dimensional and two-dimensional step-backwater hydraulic model. The model was calibrated by using the current stage-discharge relation at the USGS streamgage 05451770 on the Iowa River at County Highway E49 near Tama, Iowa, and stage and discharge data from historic flooding events that were recorded at the streamgage.

The hydraulic model was then used to compute eight water-surface profiles for flood stages at 1-foot intervals referenced to the streamgage datum and ranging from the NWS “action stage” of 11 feet (ft) to 18 ft, the stage exceeding the estimated 0.2-percent annual exceedance probability (500-year recurrence interval) flood, as determined at the USGS streamgage 05451770. The simulated water-surface profiles were then combined with a geographic information system digital elevation model to delineate the area flooded at each flood stage (water level).

In addition, potential modifications to hydraulic structures within the flood plain were modeled so any effects from the potential modifications could be evaluated. Four comparison points, which were along the flood plain, showed little to no change (less than 0.1 ft) in flood elevation from the existing conditions within the flood plain for the 11- to 16-ft stages as referenced to the USGS streamgage 05451770. There were greater changes (more than 0.1 ft) in flood elevation for the 2 comparison points that were closest to the modified hydraulic structure for the 2 highest modeled stages of 17 and 18 ft.

The availability of these maps, along with internet information regarding current stage from the USGS streamgage and forecasted high-flow stages from the NWS, will provide emergency management personnel and residents with information that is critical for flood-response activities such as evacuations and road closures, as well as for postflood recovery efforts.

Petrologic and mineral physics database for use with the U.S. Geological Survey National Crustal Model

Released June 27, 2019 11:15 EST

2019, Open-File Report 2019-1035

Theron Sowers, Oliver S. Boyd

We present a petrologic and mineral physics database as part of the U.S. Geological Survey National Crustal Model (NCM). Each of 209 geologic units, 134 of which are currently part of the geologic framework within the NCM, was assigned a mineralogical composition according to generalized classifications with some refinement for specific geologic formations. This report is concerned with the petrology and mineral physics of each geologic unit within the NCM, which control the physical behavior of the solid mineral matrix within the rock.

This mineral physics database builds on the work of Abers and Hacker to include 13 minerals specific to continental rock types. We explored the effect of this database on zero-porosity anharmonic P- and S-wave rock velocities and density relative to a well-used empirical study of relations between wavespeeds and density by Brocher. We found that empirical relations between P-wave velocity and S-wave velocity or density do well on average but can differ from mineral physics calculations by up to 15 percent in S-wave velocity and almost 40 percent in density. This is consistent with Brocher’s study where he obtained similar results for in situ measurements and laboratory rock specimens.

Additionally, the substantial presence of quartz in many rocks plays a major role in crustal seismic velocities and density due to quartz’s αβ phase transition, which can interfere with these empirical relationships. With increasing depth, quartz P-wave velocity can suddenly jump by 15 percent accompanied by little change in S-wave velocity and a modest decrease in density. Empirical relations based on observed P-wave velocity where P-wave velocity is positively correlated with S-wave velocity and density would then significantly overestimate both S-wave velocity and density.

Water resources of East Carroll Parish, Louisiana

Released June 27, 2019 10:55 EST

2019, Fact Sheet 2019-3014

Vincent E. White

Information concerning the availability, use, and quality of water in East 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, 39.63 million gallons per day (Mgal/d) of water were withdrawn in East Carroll Parish: 32.43 Mgal/d from groundwater sources and 7.20 Mgal/d from surface-water sources. Withdrawals for agricultural use—composed of general irrigation, rice irrigation, and livestock—accounted for 97 percent (38.55 Mgal/d) of the total water withdrawn. Other categories of use 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 1980 at 47.96 Mgal/d.

Hydraulic, geochemical, and thermal monitoring of an aquifer system in the vicinity of Mammoth Lakes, Mono County, California, 2015–17

Released June 27, 2019 09:48 EST

2019, Open-File Report 2019-1063

James F. Howle, William C. Evans, Devin L. Galloway, Paul A. Hsieh, Shaul Hurwitz, Gregory A. Smith, Joseph Nawikas

Since 2014, the U.S. Geological Survey has been working in cooperation with the Bureau of Land Management, Mono County, Ormat Technologies, Inc., and the Mammoth Community Water District to design and implement a groundwater-monitoring program for the proposed Casa Diablo IV Geothermal Power Project in Long Valley Caldera, California, to characterize baseline groundwater-level, water-temperature, and water-chemistry conditions at dedicated monitoring wells and municipal supply wells. The publicly available data and the analyses provided here represent quality-assured and peer-reviewed information to help with the management of the thermal and non-thermal water resources beneath and in the vicinity of the town of Mammoth Lakes, California.

The methods of data collection for continuous water levels and quarterly water-temperature profiles for two 600-foot-deep monitoring wells during 2016 through 2017 are discussed. Also discussed are the methods of water-sample collection and characterizations of the water chemistry in numerous wells in the multilayered aquifer system beneath Mammoth Lakes. Additionally, the methodology used to develop digital (mathematical) filters to remove or reduce the effects of barometric pressure and solid Earth tides on the continuous water-level records is discussed.

Digitally filtered water levels for a 2017 flow test of a deep geothermal production well are described, and various aquifer responses observed during the flow test are discussed. These are further considered in a companion evaluation of potential physical and chemical influences on the water-level data collected during the flow test.

The digitally filtered water-level data indicated that some hydraulic communication exists between the deep geothermal aquifer and shallow groundwater aquifer at the location of the flow test, northeast of Mammoth Lakes. Groundwater-chemistry data from three wells indicated that shallow groundwater naturally mixes with a small component of geothermal water along the northern periphery of the shallow aquifer system at Mammoth Lakes.

Groundwater movement and interaction with surface water near the confluence of the Platte and Elkhorn rivers, Nebraska, 2016–18

Released June 26, 2019 16:55 EST

2019, Scientific Investigations Report 2019-5048

Christopher M. Hobza, Mason J. Johnson, Paul W. Woodward, Kellan R. Strauch, Aaron R. Schepers

The State of Nebraska requires a sustainable balance between long-term water supplies and uses of groundwater and surface water and requires Natural Resources Districts to include the effect of groundwater use on surface-water systems as part of their respective integrated management plans. Recent droughts in Nebraska (2000–6; 2012–13) have amplified concerns about the long-term sustainability of groundwater and surface-water resources in the state, and concerns about the effect of groundwater irrigation on both streamflow and the water supplies needed to meet wildlife, recreational, and municipal needs. The lower Platte River provides nearly 100 percent of drinking-water supplies to Lincoln, Nebraska, 40 to 60 percent of drinking-water supplies to Omaha, Nebr., and critical aquatic and riparian habitat for threatened and endangered species. The Lower Platte River Basin-wide Management Plan has been jointly developed by the Nebraska Department of Natural Resources and seven Natural Resources Districts to address some of these concerns by managing groundwater and surface-water resources conjunctively.

To sustain flows in the lower Platte River that are needed for municipal water supplies, water managers have proposed projects aimed at temporary storage of surface water in upstream parts of the basin to mitigate periods of low flow in the lower Platte River. To increase scientific understanding and provide support for any potential future streamflow augmentation projects, the Papio-Missouri River Natural Resources District, the Lower Platte North Natural Resources District, and the Nebraska Department of Natural Resources, in cooperation with the U.S. Geological Survey, initiated this study to examine groundwater/surface-water interaction along the lower Platte and Elkhorn Rivers upstream from their confluence. The study design described herein focused on understanding seasonal characteristics of groundwater movement and interaction with surface water during periods of high groundwater demand (June through August) and low groundwater demand (all other months). Understanding how groundwater movement and interaction with surface water are affected by streamflow conditions and local groundwater demand is critical to the development of any streamflow augmentation project intended to sustain streamflow and mitigate periods of low flow in the lower Platte River.

The characteristics of groundwater movement and interaction with surface water are affected by hydrologic and local climatic conditions. For the study area, 2016–18 conditions can be broadly characterized as above normal precipitation. The flows measured at the Elkhorn River at Waterloo, Nebr., streamflow-gaging station (U.S. Geological Survey station 06800500) were above the long-term median, and the streamflow of the Platte River near Leshara, Nebr., streamflow-gaging station (06796500) remained normal or slightly above normal for the duration of this study.

Continuous streamflow and water-level data were interpreted to examine differences in groundwater movement and interaction with surface water between the Platte and Elkhorn Rivers during high and low groundwater demand periods. Although the streamflow for the Platte and Elkhorn Rivers and their tributaries was less during the high groundwater demand period, the hydraulic gradient along a transect of recorder wells was identical (0.0012 foot per foot) during the high and low groundwater demand synoptic water-level and streamflow surveys. The hydraulic gradient between the Platte and Elkhorn Rivers generally remained between 0.0011 and 0.0012 foot per foot. It can be inferred that the hydraulic gradient, which is the only temporally variable factor in Darcy’s Law, is consistent throughout the study period and that groundwater flow does not vary appreciably along this transect.

The northern part of the study area (north of the transect of recorder wells) has consistent groundwater and tributary flow from Big Slough, Rawhide Creek (Old Channel), and Rawhide Creek for low and high groundwater demand periods. In the southern part of the study area (south of the transect of recorder wells), tributary flow is more variable and dependent on local groundwater demand and flow conditions of the Platte River. Small decreases (less than 2 feet) in the groundwater levels, such as those measured during the high groundwater demand period, can have substantial changes in the streamflow in an unnamed tributary to the Elkhorn River. The streamflow measured during the high groundwater demand synoptic water-level and streamflow survey had decreased by nearly a factor of 20 when compared to the low groundwater demand period.

The volume of groundwater discharge received by the Elkhorn River was estimated by examining the changes in streamflow between measurement locations. Streamflow measurements indicate that the groundwater discharge received by the Elkhorn River in the southern part of the study area was seasonably variable, making it difficult if not impossible to estimate an annual value. In the Elkhorn River, between the Elkhorn River at Waterloo, Nebr., streamflow-gaging station and the Q Street Bridge, streamflow measurements collected during the low groundwater demand period indicated a gain of 80 cubic feet per second, which is comparable to the gain estimated using aerial thermal infrared imagery and water temperature data. Streamflow measurements collected during the high groundwater demand period indicate a loss of 80 cubic feet per second across this same reach. In assessing water supply conditions in the lower Platte River system, the term “loss” in reference to streamflow in the Elkhorn River should be used with caution. Most likely, flow from the Elkhorn River which is “lost” to the groundwater system will later discharge to surface water closer to the confluence of the Platte and Elkhorn Rivers as underflow. A calibrated groundwater flow model of the study area likely is required to predict the fate of this water and to quantify groundwater discharge during varying hydrologic conditions along this reach.

Aerial thermal infrared imagery indicated that much of the groundwater discharge in the southern part of the study area is focused across a 3-mile reach where the Elkhorn River turns southwest, perpendicular to the regional groundwater flow direction. Points of focused groundwater discharge were not detected with aerial thermal infrared imagery, indicating that groundwater discharge is diffuse rather than concentrated at focused points. Temperature-based streambed flux estimates indicated that strong regional groundwater gradients are not driving groundwater discharge and hyporheic flow is the dominant groundwater/surface-water exchange process.

Water resources of Jackson Parish, Louisiana

Released June 26, 2019 14:30 EST

2019, Fact Sheet 2019-3020

Vincent E. White

Information concerning the availability, use, and quality of water in Jackson 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, about 4.38 million gallons per day (Mgal/d) of water were withdrawn in Jackson Parish: 4.36 Mgal/d from groundwater sources and 0.02 Mgal/d from surface-water sources. Withdrawals for public-supply use accounted for about 42 percent (1.85 Mgal/d) of the total water withdrawn, and industrial use accounted for about 54 percent (2.36 Mgal/d). Other categories of use included livestock and rural domestic. Water-use data collected at 5-year intervals from 1960 to 2010 and again in 2014 indicate that water withdrawals peaked in 1975 at about 15.26 Mgal/d. The significant decrease in water use from 1975 to 1980 was caused by a reduction of 10.38 Mgal/d in withdrawals for industrial use.

Groundwater-level change for the periods 2002–8, 2008–12, and 2008–16 in the Santa Fe Group aquifer system in the Albuquerque area, central New Mexico

Released June 26, 2019 13:41 EST

2019, Scientific Investigations Map 3435

Andre B. Ritchie, Amy E. Galanter, Lucas T.S. Curry

The U.S. Geological Survey, in cooperation with the Albuquerque Bernalillo County Water Utility Authority (ABCWUA), has developed a series of maps and associated reports, beginning in 2002, that document groundwater levels in the production zone of the Santa Fe Group aquifer system beneath a large area of the City of Albuquerque, New Mexico (hereafter called the study area). Herein, we document the construction of groundwater-level change maps for representative conditions during three periods: 2002–8, 2008–12, and 2008–16.

Groundwater-elevation changes correspond to water use by the ABCWUA, with declines occurring prior to 2008 and accelerating recovery after 2008. Prior to 2008, the ABCWUA relied exclusively on groundwater from the Santa Fe Group aquifer system for municipal water supply. For the period 2002–8, near the end of the period of exclusive groundwater use, groundwater elevations in the production zone of the Santa Fe Group aquifer system declined as much as 20 to 30 feet. The largest 2002–8 groundwater-elevation declines were observed near the southeast corner of the study area and to the west of the Rio Grande. Since the ABCWUA implemented the San Juan-Chama Drinking Water Project in 2008, the proportion of municipal water supply sourced directly from surface water has increased to approximately two-thirds of the total water supply in 2016. Following initiation of this change in supply in 2008, groundwater elevations in the production zone of the Santa Fe Group aquifer system cumulatively rose as much as 20 to 30 feet by 2012 and 30 to 40 feet by 2016. The largest groundwater-elevation rises were observed near the northeast and southeast corners of the study area and to the west of the Rio Grande, whereas groundwater-elevation declines since 2008 were restricted to a localized area on the eastern margin of the study area. The area beneath the pre-flood-control-era (1971) flood plain of the Rio Grande underwent the least amount of groundwater-level change during any period, with minimal change prior to 2008 and small groundwater-elevation rises of less than 10 feet since 2008.

Assessment of shale-oil resources of the Sirte Basin Province, Libya, 2019

Released June 26, 2019 11:40 EST

2019, Fact Sheet 2019-3028

Christopher J. Schenk, Tracey J. Mercier, Cheryl A. Woodall, Phuong A. Le, Janet K. Pitman, Ronald M. Drake II, Michael E. Brownfield, Stephanie B. Gaswirth, Thomas M. Finn

Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean resources of 23.7 billion barrels of shale oil and 23 trillion cubic feet of associated gas in the onshore part of the Sirte Basin Province of Libya.

Plague positive mouse fleas on mice prior to plague outbreaks in black-tailed and white-tailed prairie dogs

Released June 26, 2019 08:04 EST

2019, Vector-Borne and Zoonotic Diseases (19)

Gebbiena M. Bron, Carly Malave, Jesse T. Boulerice, Jorge E. Osorio, Tonie E. Rocke

Plague is a lethal zoonotic disease associated with rodents worldwide. In the western United States, plague outbreaks can decimate prairie dog (Cynomys spp.) colonies. However, it is unclear where the causative agent, Yersinia pestis, of this flea-borne disease is maintained between outbreaks, and what triggers plague-induced prairie dog die-offs. Less susceptible rodent hosts, such as mice, could serve to maintain the bacterium, transport infectious fleas across a colony, or introduce the pathogen to other colonies, possibly facilitating an outbreak. Here, we assess the potential role of two short-lived rodent species, North American deer mice (Peromyscus maniculatus) and Northern grasshopper mice (Onychomys leucogaster) in plague dynamics on prairie dog colonies. We live-trapped short-lived rodents and collected their fleas on black-tailed (Cynomys ludovicianus, Montana and South Dakota), white-tailed (Cynomys leucurus, Utah and Wyoming), and Utah prairie dog colonies (Cynomys parvidens, Utah) annually, from 2013 to 2016. Plague outbreaks occurred on colonies of all three species. In all study areas, deer mouse abundance was high the year before plague-induced prairie dog die-offs, but mouse abundance per colony was not predictive of plague die-offs in prairie dogs. We did not detect Y. pestis DNA in mouse fleas during prairie dog die-offs, but in three cases we found it beforehand. On one white-tailed prairie dog colony, we detected Y. pestis positive fleas on one grasshopper mouse and several prairie dogs live-trapped 10 days later, months before visible declines and plague-confirmed mortality of prairie dogs. On one black-tailed prairie dog colony, we detected Y. pestis positive fleas on two deer mice 3 months before evidence of plague was detected in prairie dogs or their fleas and also well before a plague-induced die-off. These observations of plague positive fleas on mice could represent early spillover events of Y. pestis from prairie dogs or an unknown reservoir, or possible movement of infectious fleas by mice.

The major coral reefs of Maui Nui, Hawai‘i—distribution, physical characteristics, oceanographic controls, and environmental threats

Released June 25, 2019 15:06 EST

2019, Open-File Report 2019-1019

Michael E. Field, Curt D. Storlazzi, Ann E. Gibbs, Nicole L. D'Antonio, Susan A. Cochran

Coral reefs are widely recognized as critical to Hawaiʻi’s economy, food resources, and protection from damaging storm waves. Yet overfishing, land-based pollution, and climate change are threatening the health and sustainability of those reefs, and accordingly, both the Federal and State governments have called for protection and effective management. In 2000, the U.S. Coral Reef Task Force stated that 20 percent of coral reefs should be protected by 2010. In 2016, the Governor of Hawaiʻi committed to effective management of 30 percent of Hawaiian coastal habitats by 2030 to protect coral reefs. At present, the amount of coral protected in the main Hawaiian Islands is less than 1 percent.

Most of the large, highly diverse coral reef tracts in the main Hawaiian Islands surround the four islands of Maui, Molokaʻi, Lānaʻi, and Kahoʻolawe, collectively known as Maui Nui. This report provides fundamental information on the location, extent, coral cover, threats, and connectivity of these major coral reef tracts in Maui Nui essential for identifying areas for management and protection.

By combining high-resolution bathymetric data with available maps, publications, and satellite and underwater images, nine major coral reef tracts are identified in the coastal waters of Maui Nui. Three very large reef tracts lie along the south side of Molokaʻi, two on the east side of Lānaʻi, and four off Maui. The factors that make these Maui Nui coral reef tracts a major and important resource for Hawaiʻi include their vast size and high coral cover (nearly 16,000 acres of reef, most of which has more than 50 percent live coral cover); diversity of shape, size, and location; and separation between reefs while retaining connectivity via currents. The decline in the health of these coral reefs over the past several decades has been slow but persistent. Punctuation of the decline by large-scale disturbance events, such as the thermal bleaching that occurred in 2015, is accelerating the loss of viable reef areas by an order of magnitude.

The economic, cultural, and recreational value of these coral reef tracts highlights the importance of their long-term survival to the local communities and all of Hawaiʻi. There is scientific consensus that increasing pressures from climate change, overfishing, and land-based pollution will virtually assure the continued, and perhaps accelerating, decline of Hawaiʻi’s coral reefs unless action is taken. Information presented in this report, coupled with the results of numerous scientific studies, provides scientific underpinning to help establish a network of large-scale, connected Marine Protected Areas to meet the Federal and State governments’ call for effective management and protection of coral reefs in Maui Nui.

Satellite observations of surface deformation at the Coso Geothermal Field, California

Released June 25, 2019 13:22 EST

2019, Conference Paper, GRC Transactions

Mariana Eneva, Andrew Barbour, David Adams, Vicky Hsiao, Kelly Blake, Giacomo Falorni, Roberto Locatelli

Surface deformation time series and rates are identified at the Coso Geothermal Field (CGF) and surrounding areas by applying interferometric synthetic aperture radar (InSAR) to satellite scenes from Envisat (June 2004 ̶ October 2010) and Sentinel (November 2014 – April 2018). The measurements are done in the line of sight (LOS) to each satellite, within an area of size ~450 km2, at the locations of hundreds of thousands permanent and distributed scatterers. Thirty descending (satellite moves north to south) and 45 ascending (south to north) images were used from Envisat, and 63 descending and 65 ascending from Sentinel. A decomposition into average vertical and east horizontal components is also performed in more than 35,000 100-m pixels where both types of LOS measurements are available. The main observations at CGF include: (1) a subsidence area of size ~70 km2, with a maximum subsidence of –27.6 mm/year for the Envisat period and lower maximum subsidence of –19.1 mm/year for the Sentinel period; (2) eastward movements in the western part of the subsidence area, with Envisat maximum of +23.9 mm/year and a lower Sentinel maximum of +15.9 mm/year; (3) westward displacements in the eastern part of the subsidence area, with Envisat maximum of ̶ 14.2 mm/year and Sentinel maximum of –11.9 mm/year; (4) very good agreement of the InSAR observations with leveling survey data; (5) earthquake clusters in the subsidence area and hypocentral cross-sections showing clusters at various depths and migration in time; and (6) good predictions of the overall geothermal resource, based on poroelastic modeling using both leveling and InSAR data. The ultimate goal of the project is to provide geothermal operators with tools that can be used in reservoir management.

Integrating behavior and physiology into strategies for amphibian conservation

Released June 25, 2019 11:48 EST

2019, Frontiers in Ecology and Evolution (7)

Susan Walls, Caitlin R Gabor

The amphibian decline crisis has been challenging to address because of the complexity of factors—and their multitude of interactive effects—that drive this global issue. Dissecting such complexity could benefit from strategies that integrate multiple disciplines and address the mechanistic underpinnings of population declines and extirpations. We examine how the disciplines of behavior and physiology could be used to develop conservation strategies for amphibians and identify eight research gaps that provide future directions for the emerging fields of conservation behavior and conservation physiology. We present two case studies on imperiled salamanders that show how studies of behavior and physiology may support amphibian conservation efforts. We found several applications of stress physiology to amphibian conservation, but long-term studies are needed to understand how stress ultimately affects individual fitness and population resilience. Additionally, multiple measures of physiological health are needed to provide a more holistic assessment of an individual’s overall condition. Previous behavioral and physiological studies have been instrumental for understanding how amphibians respond to habitat modification, pathogens and parasites, contaminants, and invasive species. Some behavior-based approaches to mitigating invasive species issues have been successful in short-term studies with individual species. However, widespread application of these tactics has not yet been integrated into conservation and management strategies for ecologically-similar species. A diversity of modeling approaches has enhanced understanding of how climate change may impact amphibian populations, but model predictions need empirical tests to provide conservation managers with workable approaches to multiple perturbations associated with global environmental change. We illustrate that behavior and physiology can have broad utility for amphibian conservation, but evidence is scant that such studies have actually been used to inform strategies for amphibian conservation and management.

Landscape change associated with the upper Scenic Drive landslide, La Honda, California, January 10–June 28, 2017

Released June 25, 2019 10:35 EST

2019, Open-File Report 2019-1024

Alexandra J. Pickering, Carol S. Prentice, Stephen B. DeLong

La Honda, California, is a small town in unincorporated San Mateo County, located on the west edge of the San Francisco Peninsula in the Santa Cruz Mountains, between San Francisco and San Jose. The Scenic Drive area of La Honda has experienced several past episodes of landslide motion, which were documented in 1998, 2005, and 2006. This report documents the movement of the upper Scenic Drive landslide that occurred between January 10 and June 28, 2017. Our mapping provides a snapshot of the 2017 upper Scenic Drive landslide, as imaged from high-resolution terrestrial laser scanner (TLS) survey data (also referred to as terrestrial lidar) that we collected January 27–28, 2017; we mapped the landforms associated with the 2017 upper Scenic Drive landslide motion using a bare-earth TLS shaded-relief base map, in addition to field observations. Our mapping is supplemented by photographs of the mapped landforms, which were taken between January 11 and 31, 2017; these photographs illustrate the development of selected landslide features. The purpose of this report is to make available the maps constructed from three-dimensional TLS data and the photographs that show the landslide morphology of the 2017 upper Scenic Drive landslide. The scope of this report is limited to the motion of the upper Scenic Drive landslide that occurred between January 10 and June 28, 2017.

Establishing genome sizes of focal fishery and aquaculture species along Baja California, Mexico

Released June 25, 2019 09:50 EST

2019, Conservation Genetics Resources

Constanza del Mar Ochoa-Saloma, Jill A. Jenkins, Manuel A. Segovia, Miguel A. Del Rio-Portilla, Carmen G. Paniagua-Chavez

Genome size—the total haploid content of nuclear DNA— is constant in all cells in individuals within a species, but differs among species. Consequently, the genome size is a quantifiable genetic signature that not only characterizes a species, but it can reflect chromatin modifications, which play fundamental roles in most biological processes that are involved in the manipulation and expression of DNA. This characteristic makes the genome size a crucial parameter for genetic research on endemic aquatic species and for genetic manipulations in aquaculture species. Technologies for genetic assessments and improvements applied to fishery and aquaculture species use genome size values as a means by which hybrids, polyploids, and sex can be identified, when sex chromosomes exist. The objectives of this study were to determine genome sizes of aquatic species with economic and biological importance along the Pacific coast of Mexico, as well as to identify the appropriate reference standards for use in this study. Blood, hemolymph or milt were collected from 10 species occurring along the coast of Baja California: Sablefish Anoplopoma fimbria, Black Snapper Lutjanus novemfasciatus, California Halibut Paralichthys californicus, Pacific Sardine Sardinops sagax, Flag Rockfish Sebastes rubrivinctus, Starry Rockfish Sebastes constellatus, Totoaba Totoaba macdonaldi, Whiteleg Shrimp Litopenaeus vannamei and two Yellowtail Seriola lalandi and S. dorsalis. Nuclear DNA was stained with propidium iodide solution and the genome size was determined by flow cytometry, with results ranging from 0.61 pg (1.22 pg/diploid cell) to 2.59 pg (5.18 pg/diploid cell), with the smallest value in Sablefish and the largest in the Whiteleg Shrimp. No significant differences were detected (P ≤ 0.05) among individuals of the same species; the likely reason behind any dissimilar DNA content values with those from the literature were differences in methodologies or variations in genetics. Red-ear Slider Turtle Trachemys scripta elegans 2.65 pg (5.30 pg/diploid cell) and Red Junglefowl Gallus gallus1.27 pg (2.54 pg/diploid cell) were chosen as the standards for reference values. These results establish the basis for the Mexican National Aquatic Genetic Resources project supporting genetic improvements for aquaculture and conservation status parameters for fisheries species.

Carbon dioxide emissions and methane flux from forested wetland soils of the Great Dismal Swamp, USA

Released June 25, 2019 09:34 EST

2019, Environmental Management

Laurel Gutenberg, K.W. Krauss, John Qu, Changwoo Ahn, Dianna M. Hogan, Zhiliang Zhu, Chenyang Xu

The Great Dismal Swamp, a freshwater forested peatland, has accumulated massive amounts of soil carbon since the postglacial period. Logging and draining have severely altered the hydrology and forest composition, leading to drier soils, accelerated oxidation, and vulnerability to disturbance. The once dominant Atlantic white cedar, cypress, and pocosin forest types are now fragmented, resulting in maple-gum forest communities replacing over half the remaining area. In order to determine the effect of environmental variabes on carbon emissions, this study observes 2 years of CO2 and CH4 soil flux, which will also help inform future management decisions. Soil emissions were measured using opaque, non-permanent chambers set into the soil. As soil moisture increased by 1 unit of soil moisture content, CH4 flux increased by 457 μg CH4–C/m2/h. As soil temperature increased by 1 °C, CO2 emissions increased by 5109 μg CO2–C/m2/h. The area of Atlantic white cedar in the study boundary has an average yearly flux of 8.6 metric tons (t) of carbon from CH4 and 3270 t of carbon from CO2; maple-gum has an average yearly flux of 923 t of carbon from CH4 and 59,843 t of carbon from CO2; pocosin has an average yearly flux of 431 t of carbon from CH4 and 15,899 t of carbon from CO2. Total Cha−1year−1 ranged from 1845 kg of Cha−1year−1 in maple-gum to 2024 kg Cha−1year−1 for Atlantic white cedar. These results show that soil carbon gas flux depends on soil moisture, temperature and forest type, which are affected by anthropogenic activities.

Aquifer storage change and storage properties, 2010–2017, in the Big Chino Subbasin, Yavapai County, Arizona

Released June 24, 2019 15:18 EST

2019, Scientific Investigations Report 2019-5060

Jeffrey R. Kennedy, Libby M. Kahler, Amy M. Read

The Big Chino Subbasin is a groundwater basin that includes the Verde River headwaters in Yavapai County in north-central Arizona. Groundwater in the southern part of the subbasin is found primarily in the Big Chino and Williamson Valleys. The former is a potential municipal water source for growing communities in Yavapai County, particularly groundwater from the Big Chino Water Ranch, about 15 miles northwest of the community of Paulden. Groundwater in the Big Chino Valley discharges to wells (by pumping), by evapotranspiration, and to the upper Verde River springs, which form the headwaters of the Verde River. Groundwater also discharges to short perennial reaches of Williamson Valley Wash, Walnut Creek, and a small number of small, ungaged springs and seeps. To monitor changes in groundwater storage and to identify aquifer-storage properties, a network of repeat microgravity stations and groundwater-level monitoring stations was established in the Big Chino and Williamson Valleys in 2010.

Small decreases in groundwater storage were observed throughout the study area from 2010 to 2017. Annual groundwater withdrawals for agricultural use varied between 2,800 and 4,000 acre-ft between 2013 and 2016, with an additional amount, probably less than 1,000 acre-ft, withdrawn for domestic use, primarily in the Paulden and Williamson Valley Wash areas. No local recharge events from sustained rainfall were observed during 2010 to 2017, and base-flow discharge in the Verde River near Paulden and Williamson Valley Wash near Paulden was consistently below the long-term average (for years 1964 to 2017 and 1966 to 2017, respectively) at each site. Relations between groundwater-level changes and aquifer-storage changes (determined from repeat microgravity data) indicate monitoring wells are representative primarily of semiconfined aquifer conditions in the Paulden area, the area west of Big Chino Wash, and the Big Chino Water Ranch area. Unconfined aquifer conditions are monitored in the Williamson Valley Wash area and at two sites in the Paulden area. Specific yield was estimated at five wells and ranged between 0.04 and 0.34, with a median value of 0.23. 

Negative groundwater-level trends (increasing depth to water) were observed between 2010 and 2017 at all sites where trends were identified using the Mann-Kendall trend test, except for the northernmost reaches of Big Chino Wash within and to the north of the Big Chino Water Ranch. Groundwater storage trends were negative at all sites where trends were identified except for one site in the foothills of the Santa Maria mountains west of Big Chino Wash. Declining storage in the Big Chino Water Ranch area, where water levels show no trend or are increasing, are likely the result of drying conditions in the unsaturated zone and (or) aquifers located above the aquifer(s) monitored by wells.

Improved detection of rare, endangered and invasive trout using a new large-volume sampling method for eDNA capture

Released June 24, 2019 12:34 EST

2019, Environmental DNA

Adam J. Sepulveda, Jenna Schabacker, Seth Smith, Robert Al-Chokhachy, Gordon Luikart, Stephen J. Amish

Environmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restricts the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may be to collect fewer, large volume water samples using coarse filters that do not clog as rapidly. We used mesocosm experiments and field evaluations to compare coarse filter-large water volume samples (hereafter large volume filter samples) vs. fine filter-small water volume samples (hereafter small volume filter samples) for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. We found that large volume filter sampling can be an effective approach for detecting DNA of low density target taxa. In mesocosm experiments, large volume and small volume water samples detected similar quantities of rainbow trout DNA. In the field, large volume samples more frequently detected bull trout DNA, had higher bull trout DNA copy number, and higher total DNA concentrations than small volume samples. However, sampling higher water volumes increased the potential for PCR inhibition so the DNA workflow had to be altered for large volume samples. Combining larger water volume samples with other strategies, like increasing PCR sensitivity and the number of PCR replicates, will improve detection of rare species, which is crucial for advancing conservation and ecological understanding.

Supply chain infrastructure restoration calculator software tool—Developer guide and user manual

Released June 24, 2019 11:58 EST

2019, Open-File Report 2019-1061

Akhilesh Ojha, Bhanu Kanwar, Suzanna K. Long, Thomas G. Shoberg, Steven Corns

This report describes a software tool that calculates costs associated with the reconstruction of supply chain interdependent critical infrastructure in the advent of a catastrophic failure by either outside forces (extreme events) or internal forces (fatigue). This tool fills a gap between search and recover strategies of the Federal Emergency Management Agency (or FEMA) and construction techniques under full recovery. In addition to overall construction costs, the tool calculates reconstruction needs in terms of personnel and their required support. From these estimates, total costs (or the cost of each element to be restored) can be calculated. Estimates are based upon historic reconstruction data, although decision managers do have the choice of entering their own input data to tailor the results to a local area.

ModelMuse Version 4: A graphical user interface for MODFLOW 6

Released June 24, 2019 10:00 EST

2019, Scientific Investigations Report 2019-5036

Richard B. Winston

ModelMuse, a graphical user interface for groundwater-modeling software, was modified to support MODFLOW 6. ModelMuse works with two types of spatial discretization in MODFLOW 6: structured grids (DIS) and discretization by vertices (DISV). Quadtree refinement is used to generate a DISV model from a structured-grid model. The locations and weights for ghost nodes used to improve DISV model accuracy are computed automatically by ModelMuse using a new algorithm. ModelMuse does not support other types of DISV grids and unstructured grids. ModelMuse supports options in MODFLOW 6 that designate individual cells as confined or convertible and remove inactive cells associated with discontinuous layers, thereby reducing the computational burden. ModelMuse can specify fully three-dimensional (3D), spatially variable anisotropy in hydraulic conductivity. Although MODFLOW 6 does not support the parameters supported by MODFLOW–2005, ModelMuse provides backward compatibility by allowing ModelMuse parameters to specify scale-factor variables in MODFLOW 6 time-series files within packages that support time-series files. ModelMuse can automatically convert the data for many of the packages from other MODFLOW models to the new data for these packages in MODFLOW 6. Some packages, such as the Streamflow-Routing (SFR) package, changed significantly enough that only a partial conversion is possible. Head and flow observations in older models are also converted to observation locations in the MODFLOW 6 Observation utility. ModelMuse accommodates the ability of MODFLOW 6 to store specific discharge components by allowing the user to visualize the components of a specific discharge on the model grid. ModelMuse supports the versions of MODPATH and ZONEBUDGET compatible with MODFLOW 6.

Densities, diets, and growth rates of larval Alewife and Bloater in a changing Lake Michigan ecosystem.

Released June 24, 2019 09:37 EST

2019, Transactions of the American Fisheries Society

Drew E Eppehimer, David Bunnell, Patricia Armenio, David Warner, Lauren A. Eaton, David J Wells, Edward S. Rutherford

Variability in abiotic and biotic factors during larval stages has profound impacts on fish recruitment. In Lake Michigan, where the composition of lower trophic levels has undergone considerable changes in the past decade, managers are concerned that fish recruitment could be negatively affected. We hypothesized that spatial variation in Lake Michigan larval fish density and growth can be explained by various environmental predictor variables. In July 2015, we sampled larval fish and zooplankton at 24 sites (distributed among eight transects) around Lake Michigan. We measured larval fish densities and estimated growth rates and diets of the two most abundant species: the Alewife Alosa pseudoharengus and Bloater Coregonus hoyi (prey fish that represented 89% and 4% of the total catch, respectively). Larval Alewife densities at a given site ranged from 0 to 42.57 larvae/100 m3, but no explanatory variables explained the variation. Alewife mean growth rate equaled 0.50 mm/d, and fish age and zooplankton density best explained growth variation across sites. Larval Bloater densities ranged from 0 to 1.16 larvae/100 m3, and mean growth rate was 0.21 mm/d. Across all sites, 67% of larval Alewife stomachs were empty, whereas only 16% of Bloater stomachs were empty. Larval fish growth rates observed in our study were at least 40% slower than those reported in previous decades for both Alewife and Bloater. Worsening prey environment for pelagic larvae, such as Alewife and Bloater, during the era of abundant dreissenid mussels could reduce the probability of strong year‐classes, which in turn may affect growth and survival of recreationally important salmonine predators.

The evolving threat of rapid Ohia death (ROD) to Hawaii’s native ecosystems and rare plant species

Released June 24, 2019 09:23 EST

2019, Forest Ecology and Management (448) 376-385

Lucas B. Fortini, Lauren R. Kaiser, Lisa Keith, Jonathan Price, R. Flint Hughes, James D. Jacobi, J. B. Friday

Hawai‘i’s most widespread native tree, ‘ōhi‘a lehua (Metrosideros polymorpha), has been dying across large areas of Hawai‘i Island mainly due to two fungal pathogens (Ceratocystis lukuohia and Ceratocystis huliohia) that cause a disease collectively known as Rapid ‘Ōhi‘a Death (ROD). Here we examine patterns of positive detections of C. lukuohia as it has been linked to the larger mortality events across Hawai‘i Island. Our analysis compares the environmental range of C. lukuohia and its spread over time through the known climatic range and distribution of ‘ōhi‘a. Analyses show this fungal pathogen generally encompassed the core, but not the extremes of the climatic range of ‘ōhi‘a. We further modeled the potential distribution of C. lukuohiaacross the Hawaiian Archipelago to estimate the risk of ROD to other islands. Given the potential for C. lukuohia to alter the structure of ‘ōhi‘a dominated forests, we used our projected potential distribution of C. lukuohia to assess the risk of ROD to threatened and endangered plant species across Hawai‘i. Many native plants are likely vulnerable to these types of large ‘ōhi‘a mortality events: of 234 endangered native plant species considered, 147 (62.8%) have more than half of their range within current and expanding C. lukuohia suitable areas. We also found evidence that protecting habitat by fencing out introduced feral ungulates reduces the prevalence of the disease likely by reducing physical damage caused by these animals to ‘ōhi‘a trees, a precondition for Ceratocystis infection. Given the ongoing spread of C. lukuohia, we developed a dynamic web portal to host our results online, where models and analyses are updated with new lab-confirmed detections to provide managers with a useful tool to help monitor and assess the risk of C. lukuohia as it continues to spread.