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Publications recently added to the Pubs Warehouse

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Social–ecological mismatches create conservation challenges in introduced species management

Released March 20, 2019 16:24 EST

2019, Frontiers in Ecology and the Environment (17) 117-125

Erik A. Beever, Daniel Simberloff, Sarah L. Crowley, Robert Al-Chokhachy, Hazel A. Jackson, Steven L. Petersen

Introduced species can have important effects on the component species and processes of native ecosystems. However, effective introduced species management can be complicated by technical and social challenges. We identify “social–ecological mismatches” (that is, differences between the scales and functioning of interacting social and ecological systems) as one such challenge. We present three case studies in which mismatches between the organization and functioning of key social and ecological systems have contributed to controversies and debates surrounding introduced species management and policy. We identify three common issues: social systems and cultures may adapt to a new species’ arrival at a different rate than ecosystems; ecological impacts can arise at one spatial scale while social impacts occur at another; and the effects of introduced species can spread widely, whereas management actions are constrained by organizational and/or political boundaries. We propose strategies for collaborative knowledge building and adaptive management that may help address these challenges.

Downstream‐propagating channel responses to decadal‐scale climate variability in a glaciated river basin

Released March 20, 2019 14:49 EST

2019, Journal of Geophysical Research: Earth Surface

Scott W. Anderson, Christopher P. Konrad

Regional climate is an important control on the rate of coarse sediment mobilization and transport in alpine river systems. Changes in climate are then expected to cause a cascade of geomorphic responses, including adjustments in downstream channel morphology. However, the mechanics and sensitivity of channel response to short‐term climate variability remain poorly documented. In the Nooksack River, which drains a glaciated stratovolcano in Washington State, bed elevation changes were inferred from shifting stage–discharge relations at seven USGS stream gages. Decadal‐scale elevation trends at most sites can be explained as a downstream‐propagating channel response to regional climate variability, where periods of persistent warm, dry [cool, wet] conditions corresponded to periods of aggradation [incision]. The channel elevation response propagated downstream at a rate of one to four kilometers per year; propagation rate scaled closely with channel slope. Historical trends in glacier extent and flood intensity both show some potential to explain climate–sediment linkages, though assessing causation is complicated by the shared climate signal in both records. Results show the influence of the Pacific Decadal Oscillation, with relatively high coarse sediment yields prior to 1950 and since 1980, and notably lower sediment yields from 1950 to 1980. Measured sediment yields from nearby glaciated basins corroborate this history, suggesting a regional coherence to these climate–sediment linkages. These results document consistent relations between climate, sediment supply and downstream channel response at the basin‐scale, with channel responses propagating downstream over periods of decades with little apparent attenuation.

Defining the limits of spectrally based bathymetric mapping on a large river

Released March 20, 2019 14:45 EST

2019, Remote Sensing (11) 1-29

Carl J. Legleiter, Ryan L. Fosness

Remote sensing has emerged as a powerful method of characterizing river systems but is subject to several important limitations. This study focused on defining the limits of spectrally based mapping in a large river. We used multibeam echosounder (MBES) surveys and hyperspectral images from a deep, clear-flowing channel to develop techniques for inferring the maximum detectable depth, dmax , directly from an image and identifying optically deep areas that exceed dmax . Optimal Band Ratio Analysis (OBRA) of progressively truncated subsets of the calibration data provided an estimate of dmax by indicating when depth retrieval performance began to deteriorate due to the presence of depths greater than the sensor could detect. We then partitioned the calibration data into shallow and optically deep ( d>dmax ) classes and fit a logistic regression model to estimate the probability of optically deep water, Pr(OD) . Applying a Pr(OD) threshold value allowed us to delineate optically deep areas and thus only attempt depth retrieval in relatively shallow locations. For the Kootenai River, dmax reached as high as 9.5 m at one site, with accurate depth retrieval ( R2=0.94 ) in areas with d<dmax . As a first step toward scaling up from short reaches to long river segments, we evaluated the portability of depth-reflectance relations calibrated at one site to other sites along the river. This analysis highlighted the importance of calibration data spanning a broad range of depths. Due to the inherent limitations of passive optical depth retrieval in large rivers, a hybrid field- and remote sensing-based approach would be required to obtain complete bathymetric coverage.

Regression Models for Estimating Sediment and Nutrient Concentrations and Loads at the Kankakee River, Shelby, Indiana, December 2015 through May 2018

Released March 20, 2019 14:45 EST

2019, Scientific Investigations Report 2019-5005

Timothy R. Lathrop, Aubrey R. Bunch, Myles S. Downhour

The Kankakee River in northern Indiana flows through the area once known as the Grand Marsh. Beginning in the 1860s, anthropogenic changes to the river within Indiana resulted in downstream flooding and additional transport of sediment and nutrients. In 2015, the U.S. Geological Survey, in cooperation with the Indiana Department of Environmental Management, upgraded the gaging station Kankakee River at Shelby, Indiana, to include the collection of water-quality data. By relating continuously monitored water-quality data to discrete data collected from December 2015 through May 2018, linear regression was used to develop models for estimating concentrations of suspended sediment, total nitrogen, and total phosphorus. Developed regression models indicated a strong correlation between turbidity and specific conductance with suspended-sediment concentration (adjusted coefficient of determination equals 0.92, predicted residual error sum of squares equals 0.151), nitrate plus nitrite and specific conductance with total nitrogen (adjusted coefficient of determination equals 0.95, predicted residual error sum of squares equals 0.0248), and turbidity with total phosphorus (adjusted coefficient of determination equals 0.89, predicted residual error sum of squares equals 0.0103).

Daily loads of suspended sediment, total nitrogen, and total phosphorus were computed as the product of daily mean regression model concentrations and daily mean streamflow. Rloadest models were used to compute daily loads of each constituent during gaps in regression model loads. For 2016 and 2017, the estimated annual suspended-sediment loads were 105,000 and 91,000 tons; estimated total nitrogen loads were 8,690 and 8,890 tons; and estimated total phosphorus loads were 265 and 236 tons, respectively.

State-space analysis of power to detect regional brook trout population trends over time

Released March 20, 2019 14:42 EST

2019, Canadian Journal of Fisheries and Aquatic Sciences

Kasey C. Pregler, R. Daniel Hanks, Evan S. Childress, Nathaniel P. Hitt, Daniel J. Hocking, Benjamin H. Letcher, Yoichiro Kanno

Threats to aquatic biodiversity are expressed at broad spatial scales, but identifying regional trends in abundance is challenging owing to variable sampling designs, and temporal and spatial variation in abundance. We compiled a regional dataset of brook trout Salvelinus fontinalis counts across their southern range representing 326 sites from eight states between 1982-2014, and conducted a statistical power analysis using Bayesian state-space models to evaluate the ability to detect temporal trends by characterizing posterior distributions with three approaches. A combination of monitoring periods, number of sites and electrofishing passes, decline magnitude and different revisit patterns were tested. Power increased with monitoring periods and decline magnitude. Trends in adults were better detected than young-of-the-year fish, which showed greater inter-annual variation in abundance. The addition of weather covariates to account for the temporal variation increased power only slightly. Single- and three-pass electrofishing methods were similar in power. Finally, power was higher for sampling designs with more frequent revisits over the duration of the monitoring program. Our results provide guidance for broad-scale monitoring designs for temporal trend detection.

User’s manual for the Draper climate-distribution software suite with data‑evaluation tools

Released March 20, 2019 11:25 EST

2019, Techniques and Methods 7-C22

John M. Donovan, Kathryn M. Koczot

Development of a time series of spatially distributed climate data is an important step in the process of developing physically based environmental models requiring distributed inputs of climate data beyond what is available from observations collected at climate stations. To prepare inputs required for model-mapping units across the study area, climate data (temperature and precipitation) are distributed by combining data from gridded surfaces of mean-monthly climate-data values with (often) widely spaced daily point observations. Examples of climate-data files used to develop PRMS-formatted input files for the Merced River Basin Precipitation-Runoff Modeling System (PRMS) are included in this manual.

The Draper Climate-Distribution Software Suite (Draper Suite) consists of the Draper climate-distribution program (Draper) and several supporting pre- and post-processing applications. Draper combines spatially distributed input in the form of monthly averaged values for precipitation, maximum temperature, and minimum temperature with daily observed data from climate stations to estimate distributed climate-data values at predefined locations across a study area (typically a drainage basin) on a daily time step. Alternative methods are used when station data are limited or missing for a particular day. Draper uses a set of required and optional input and output files with defined formats and naming conventions. A shell application also is available to manage multiple runs of the Draper application.

Other applications in the Draper Suite include (1) a tool to find and interactively remove outliers in the input data, (2) a tool to check and enforce a minimum daily temperature range, and (3) a tool to view output diagnostic information as time-series graphs. These tools can be used iteratively to evaluate and improve the results from Draper as part of a workflow involving physically based environmental models, such as the Precipitation-Runoff Modeling System (PRMS).

Quality of surface water in Missouri, water year 2017

Released March 19, 2019 11:02 EST

2019, Data Series 1108

Miya N. Barr, Katherine A. Bartels

The U.S. Geological Survey, in cooperation with the Missouri Department of Natural Resources, designed and operates a network of monitoring stations on streams and springs throughout Missouri known as the Ambient Water-Quality Monitoring Network. During water year 2017 (October 1, 2016, through September 30, 2017), data presented in this report were collected at 72 stations: 70 Ambient Water-Quality Monitoring Network stations and 2 U.S. Geological Survey National Stream Quality Assessment Network stations. Among the 72 stations in this report, 4 stations have data presented from additional sampling performed in cooperation with the U.S. Army Corps of Engineers. Summaries of the concentrations of dissolved oxygen, specific conductance, water temperature, suspended solids, suspended sediment, Escherichia coli bacteria, fecal coliform bacteria, dissolved nitrate plus nitrite as nitrogen, total phosphorus, dissolved and total recoverable lead and zinc, and selected pesticide compounds are presented. Most of the stations have been classified based on the physiographic province or primary land use in the watershed represented by the station. Some stations have been classified based on the unique hydrology of the waterbodies they monitor. A summary of hydrologic conditions in the State including peak streamflows, monthly mean streamflows, and 7-day low flows also are presented.

Dynamic flood modeling essential to assess the coastal impacts of climate change

Released March 18, 2019 16:40 EST

2019, Scientific Reports (9) 1-13

Patrick L. Barnard, Li H. Erikson, Amy C. Foxgrover, Juliette A. Finzi Hart, Patrick W. Limber, Andrea C. O'Neill, Maarten van Ormondt, Sean Vitousek, Nathan J. Wood, Maya K. Hayden, Jeanne M. Jones

Coastal inundation due to sea level rise (SLR) is projected to displace hundreds of millions of people worldwide over the next century, creating significant economic, humanitarian, and national-security challenges. However, the majority of previous efforts to characterize potential coastal impacts of climate change have focused primarily on long-term SLR with a static tide level, and have not comprehensively accounted for dynamic physical drivers such as tidal non-linearity, storms, short-term climate variability, erosion response and consequent flooding responses. Here we present a dynamic modeling approach that estimates climate-driven changes in flood-hazard exposure by integrating the effects of SLR, tides, waves, storms, and coastal change (i.e. beach erosion and cliff retreat). We show that for California, USA, the world’s 5th largest economy, over $150 billion of property equating to more than 6% of the state’s GDP and 600,000 people could be impacted by dynamic flooding by 2100; a three-fold increase in exposed population than if only SLR and a static coastline are considered. The potential for underestimating societal exposure to coastal flooding is greater for smaller SLR scenarios, up to a seven-fold increase in exposed population and economic interests when considering storm conditions in addition to SLR. These results highlight the importance of including climate-change driven dynamic coastal processes and impacts in both short-term hazard mitigation and long-term adaptation planning.

Seasonal assembly of arthropod communities on milkweeds experiencing simulated herbivory

Released March 18, 2019 16:37 EST

2019, Arthropod-Plant Interactions (13) 99-108

Ian S. Pearse, Marshall McMunn, Louie H. Yang

The seasonal assembly of arthropod communities is shaped by biotic and abiotic aspects of the habitat that limit the appearance or activity phenology of potential community members. In addition, previous interactions within the community, such as herbivore-induced plant defensive responses, aggregation, and predator avoidance likely affect the assembly of arthropod communities on individual plants. We observed the phenology of arthropod communities and defensive plant traits on 100 milkweed (Asclepias eriocarpa) individuals at monthly intervals over a growing season. We experimentally wounded a subset of plants each month (April–August) to observe the effect of simulated added herbivore damage on the seasonal assembly of these arthropod communities. All plant traits and measures of arthropod communities changed over the season. The observed response to experimental leaf damage suggested a trend of induced susceptibility in early months, but not late months. Plants receiving early-season simulated herbivory experienced more subsequent leaf damage than unmanipulated plants. We observed several lagged correlations in our study indicating that blue milkweed beetle (Chrysochus cobaltinus) abundance was lower in months following high natural leaf damage, and that the abundance of a secondary omnivore (Lygaeus kalmii) and total predator abundance tended to follow months with high C. cobaltinus abundance. Ahistorical habitat factors determined much of the observed seasonality of arthropod communities, but induced responses to simulated herbivory also contributed historical effects that influenced arthropod community assembly.

Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies

Released March 18, 2019 16:35 EST

2019, AIMS Microbiology (5) 62-76

Dawn B. Goldsmith, Zoe A. Pratte, Christina A. Kellogg, Sara E. Snader, Koty H. Sharp

The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. To assess the impact of methodology on the detectable diversity of the coral’s microbiome, we obtained near full-length Sanger sequences from clone libraries constructed from a subset of the same A. poculata samples. Eight samples were analyzed: two sets of paired symbiotic (brown) and aposymbiotic (white) colonies collected in the fall (September) and two sets collected in the spring (April). Analysis of the Sanger sequences revealed that the microbiome of A. poculataexhibited a high level of richness; 806 OTUs were identified among 1390 bacterial sequences. While the Illumina study revealed that A. poculata’s microbial communities did not significantly vary according to symbiotic state, but did vary by season, Sanger sequencing did not expose seasonal or symbiotic differences in the microbiomes. Proteobacteria dominated the microbiome, forming the majority (55% to 80%) of classifiable bacteria in every sample, and the five bacterial classes with the highest mean relative portion (5% to 35%) were the same as those determined by prior Illumina sequencing. Sanger sequencing also captured the same core taxa previously identified by next-generation sequencing. Alignment of all sequences and construction of a phylogenetic tree revealed that both sequencing methods provided similar portrayals of the phylogenetic diversity within A. poculata’s bacterial associates. Consistent with previous findings, the results demonstrated that the Astrangia microbiome is stable notwithstanding the choice of sequencing method and the far fewer sequences generated by clone libraries (46 to 326 sequences per sample) compared to next-generation sequencing (3634 to 48481 sequences per sample). Moreover, the near-full length 16S rRNA sequences produced by this study are presented as a resource for the community studying this model system since they provide necessary information for designing primers and probes to further our understanding of this coral’s microbiome.

The Missouri groundwater-level observation network

Released March 18, 2019 14:30 EST

2019, Fact Sheet 2019-3009

David C. Smith

The Missouri groundwater-level observation well network is a series of wells across the State of Missouri in which groundwater levels are monitored in real time and periodically. The wells monitor the water levels in multiple key aquifers, such as the Ozark aquifer in the Salem and Springfield Plateaus and the Mississippi Alluvial Plain aquifer in the South-eastern Lowlands. As of 2018, 150 real-time sites are operated as a cooperative effort between the Missouri Department of Natural Resources (MoDNR) and the U.S. Geological Survey. This fact sheet describes the network and well data from the network.

Characterizing 12 years of wildland fire science at the U.S. Geological Survey: Wildland Fire Science Publications, 2006–17

Released March 18, 2019 12:15 EST

2019, Open-File Report 2019-1002

Paul F. Steblein, Mark P. Miller

Wildland fire characteristics, such as area burned, number of large fires, burn intensity, and fire season duration, have increased steadily over the past 30 years, resulting in substantial increases in the costs of suppressing fires and managing damages from wildland fire events (National Academies of Sciences, Engineering, and Medicine, 2017). Wildland fire management could benefit from sound decision making based on reliable scientific information. Fire scientists produce data, tools, and information to support fire and land management decision making. With ever-changing land use scenarios, environmental conditions, and emerging technological capabilities, new assessments and studies are continually needed. Established by Congress in 1879, the U.S. Geological Survey (USGS) is the primary science branch of the Department of the Interior (DOI), which manages more than 400 million acres of public lands in the United States. The USGS has more than 100 scientists across seven Mission Areas that help address the wildland fire science needs of DOI bureaus and their stakeholders. The diverse expertise of these scientists allows them to address complex interdisciplinary challenges. In this report, we identify and characterize scientific literature produced by USGS scientists during 2006–17 that addresses topics associated with wildland fire science. Our goals were to (1) make the most complete list possible of product citations readily available in an organized format, and (2) use bibliometric analysis approaches to highlight the productivity of USGS scientists and the impact of contributions that the Bureau has provided to the scientific, land management, and fire management communities.

Biogeochemical and physical processes controlling mercury methylation and bioaccumulation in Lake Powell, Glen Canyon National Recreation Area, Utah and Arizona, 2014 and 2015

Released March 18, 2019 11:32 EST

2019, Open-File Report 2018-1159

David L. Naftz, Mark Marvin-DiPasquale, David P. Krabbenhoft, George Aiken, Eric S. Boyd, Christopher H. Conaway, Jacob M. Ogorek, Gregory M. Anderson

Mercury monitoring results from about 300 Morone saxatilis (striped bass) muscle tissue samples collected by the State of Utah from Lake Powell resulted in a Utah/Arizona fish consumption advisory issued in 2012 for approximately the lower 100 kilometers of the reservoir. Chemical, physical, and biological data were collected during two synoptic sampling cruises on Lake Powell during May/June 2014 and August 2015 to test three hypotheses associated with a conceptual model developed to explain the observed geographic concentration gradient of Hg in fish tissue samples. This model proposes that in the transition from a primarily riverine system to a reservoir, there is a change in the concentration and composition of water-column particulate material, increasing in the proportion of organic content moving downstream, as the larger size fractions of the inorganic particulate load are deposited in the upper reservoir. This change alleviates light limitation of phytoplankton production and leads to a higher proportion of autochthonous primary production in the downstream direction. This, in turn, drives increased microbial methylmercury (MeHg) production in the benthos and potentially the water column, in the downstream direction, and results in the observed elevated fish Hg levels in the lower part of the reservoir. The model also proposes that there are differences between the main stem of Lake Powell and side canyons, embayments, or secondary rivers entering the reservoir, in terms of Hg cycling dynamics and bioaccumulations, driven mainly by differences in hydrology. Finally, seasonal differences in Hg dynamics within the reservoir are proposed, based on seasonal dynamics associated with primary production and the physical process of seasonal stratification.

A total of three statistically testable hypotheses were proposed and postulated that measurable differences in key Hg and non-Hg metrics exist between: (1) the upper and lower reservoir; (2) main stem and river arm/side canyon/embayment sites; and (3) early-season (May/June 2014, less stratified) and late-season (August 2015, stratified) conditions. Statistically modeled least square means in combination with the graphical analysis of Hg and non-Hg parameters were used to examine the data collected during the study and test these hypotheses. Data collected during the study are included in a U.S. Geological Survey data release and are available online at https://doi.org/10.5066/F74X560J.

In general, water-column, plankton, and surface sediment samples collected during the synoptic sampling cruises are supportive of the three hypotheses associated with the conceptual model. In support of hypothesis 1 (comparing upper and lower reservoir sites), the least square mean for turbidity was higher in the upper reservoir. In contrast, surface water particulate organic carbon (as a percentage of total particulate mass), particulate MeHg (by mass [in nanograms per gram] and as a percentage of total mercury [THg]), and particulate-dissolved partitioning coefficients for THg and MeHg were higher in the lower reservoir. Plankton THg concentrations also were significantly (probability [p] less than (<) 0.05) higher in the lower reservoir. Surface sediment metrics in support of hypothesis 1 include higher MeHg production potential rates in the lower reservoir. In contrast, there were no statistically significant differences between the upper and lower reservoir for surface sediment percent of MeHg and MeHg concentration, percent MeHg, or methylation rate constants. These spatial trends associated with hypothesis 1 indicate a pathway for enhanced Hg bioavailability in the lower reservoir.

Hypothesis 2, which tested for differences between main stem and river arm/side canyon/embayment sites, was supported by a number of water-column parameters, including particulate THg and MeHg concentrations by mass (in nanograms per gram) and percent particulate MeHg being significantly (p<0.05) higher in the river arms, side canyons, and embayments relative to the main stem channel. Plankton MeHg concentrations (by mass [in nanograms per gram] and volume [in nanograms per liter] and as a percentage of THg) were elevated in river arm/side canyon/embayment sites compared to main stem sites, indicating an enhanced potential for MeHg bioaccumulation at the base of the pelagic food web in river arms, side canyons, and embayments. In contrast, few of the sediment metrics differed between main stem and river arm/side canyon/embayment sampling sites; however, the potential for MeHg degradation in surface sediment was significantly higher in the main stem. The data indicate that river arm/side canyon/embayment sites may experience enhanced Hg bioaccumulation, compared to the main stem, because of higher MeHg levels at the base of the pelagic food web. This conclusion is supported by the elevated Hg detected in striped bass muscle tissue samples collected in the San Juan Arm during this study (2014). Fish collected from the lower reservoir exhibited a distinct Hg isotopic signature that was enriched in delta (δ)202Hg and capital delta (Δ)199Hg relative to fish samples collected from either Good Hope Bay or the San Juan Arm.

Hypothesis 3 tested for differences between early (May/June) high-flow and late (August) low-flow seasons. This test was supported by a range of non-Hg metrics (nitrate, phosphate, chlorophyll a, dissolved oxygen, fluorescent dissolved organic matter, temperature, and pH) that reflect the increase in chlorophyll a, decrease in nutrients, and buildup of stratified conditions in the transition from early- to late-season sampling periods. Significant seasonal differences also were noted for multiple Hg metrics, including (a) water-column filtered and particulate (by mass) MeHg and THg concentrations; (b) plankton MeHg and THg concentration (by mass); and (c) sediment percent MeHg, Hg(II)-methylation rate constant, and microbial ribosomal ribonucleic acid, small subunit 16 (16S rRNA) abundance, all of which were higher during the late-season synoptic sampling. Overall, the surface sediment metrics are consistent with a seasonal shift from the early-season synoptic results, when the availability of Hg(II) exerts a primary control on MeHg production, to the late-season synoptic sampling, when microbial activity is a dominant driver of MeHg production.

Vegetation and precipitation shifts interact to alter organic and inorganic carbon storage in cold desert soils

Released March 18, 2019 10:18 EST

2019, Ecosphere (10)

David P. Huber, Kathleen A. Lohse, Amy Commendador, Stephen Joy, Ken A. Aho, Bruce P. Finney, Matthew J. Germino

Dryland ecosystems are experiencing shifts in rainfall and plant community composition, which are expected to alter cycling and storage of soil carbon (C). Few experiments have been conducted to examine long‐term effects on (1) soil organic C (SOC) pools throughout the soil profile, and (2) soil inorganic C (SIC) pools as they relate to dynamic changes in C storage and climate change. We measured SOC and SIC from 0 to 1 m beneath plants and in adjacent interplant microsites following nearly 20 yr of experimental manipulations of plant community (native sagebrush steppe or monoculture of exotic crested wheatgrass) and the amount and timing of water availability (ambient, or doubling of annual rainfall in the dormant, DORM, or growing, GROW, season). Under sagebrush plants, GROW increased both SOC and SIC pools, resulting in total carbon (TC) pools 15% greater than plots receiving ambient precipitation, while DORM decreased SOC and SIC pools, decreasing TC pools 20% from ambient. Under crested wheatgrass plants, GROW increased SOC by 73% but decreased SIC by 11% relative to ambient, netting no change in TC pools, while DORM SIC pools were 5% greater than ambient, with no significant increase in either SOC or TC pools. GROW significantly increased TC pools for interplant microsites, regardless of vegetation treatment. At the community scale and summing C pools weighted by percent patch cover, patterns of TC pool were similar to plot measurements. Our findings suggest that sagebrush communities can become a net C source to the atmosphere with increases in dormant season rainfall rather than a C sink as previously predicted. We also provide evidence of SIC as an important and dynamic C sequestration mechanism in drylands. Consideration of vegetation type, all or most of the soil profile, and both organic and inorganic C pools are all important to accurately predict C sequestration with changing climate and disturbance in drylands.

Detection of Bisgaard taxon 40 in Rhinoceros Auklets (Cerorhinca monocerata) with pneumonia and septicemia from a mortality event in Washington, USA

Released March 15, 2019 10:50 EST

2019, Journal of Wildlife Diseases (55) 246-249

Susan N. Knowles, Barbara Bodenstein, Brenda M. Berlowski-Zier, Susan M Thomas, Scott F Pearson, Jeffrey M. Lorch

We isolated Bisgaard taxon 40 from Rhinoceros Auklets (Cerorhinca monocerata) with pneumonia and septicemia from Washington, US, found dead in 2016. Previously isolated only from the respiratory tract of a gull (Laridae), little is known about its pathogenic potential and whether it acts as a primary or opportunistic pathogen.

Manipulating wild and tamed phytobiomes: Challenges and opportunities

Released March 14, 2019 16:36 EST

2019, Phytobiomes Journal

Terrence H. Bell, Kevin L. Hockett, Ricardo Ivan Alcalá-Briseño, Mary Barbercheck, Gwyn A. Beattie, Mary Ann Bruns, John E. Carlson, Taejung Chung, Alyssa Collins, Bryan Emmett, Paul Esker, Karen Garrett, Leland Glenna, Beth K. Gugino, Maria del Mar Jimenez-Gasco, Linda Kinkel, Jasna Kovac, Kurt P. Kowalski, Gretchen Kuldau, Johan H. J. Leveau, Matthew J. Michalska-Smith, Jessica Myrick, Kari Peter, Maria Fernanda Vivanco Salazar, Ashley Shade, Nejc Stopnisek, Xiaoquing Tan, Amy T. Welty, Etienne Yergeau, Kyle Wickings

This white paper presents a series of perspectives on current and future phytobiome management, discussed at the Wild and Tamed Phytobiomes Symposium in University Park, PA, USA, in June 2018. To enhance plant productivity and health, and to translate lab- and greenhouse-based phytobiome research to field applications, the academic community and end-users need to address a variety of scientific, practical, and social challenges. Prior discussion of phytobiomes has focused heavily on plant-associated bacterial and fungal assemblages, but the phytobiomes concept covers all factors that influence plant function. Here we discuss various management considerations, including abiotic conditions (e.g. soil, nutrient applications), microorganisms (e.g. bacterial and fungal assemblages, bacterial and fungal inoculants, viruses), macroorganisms (e.g. arthropods, plant genetics), and societal factors (e.g. communication approaches, technology diffusion). An important near-term goal for this field should be to estimate the potential relative contribution of different components of the phytobiome to plant health, as well as the potential and risk of modifying each in the near-future.

Detrital K-feldspar Pb isotopic evaluation of extraregional sediment transported through an Eocene tectonic breach of southern California's Cretaceous batholith

Released March 14, 2019 16:30 EST

2019, Earth and Planetary Science Letters (508) 4-17

Danielle Ziva Shulaker, Marty Grove, Jeremy K. Hourigan, Nicholas Van Buer, Glenn R. Sharman, Keith A. Howard, Jonathan Miller, Andrew P. Barth

Sedimentary provenance studies have come to be overwhelmingly based upon U–Pb geochronologic measurements performed with detrital zircon while alternative and potentially complementary approaches such as conglomerate clast studies and heavy mineral analysis have faded in importance. Measurement of Pb isotopic compositions in detrital K-feldspar is among the under-utilized approaches available to ascertain sedimentary source regions. While it has been long recognized that common Pb isotope compositions recorded by K-feldspar vary widely and reflect the crustal provinces from which the host basement rocks crystallized, use of the approach has suffered due to a lack of appropriate statistical models and ground truth compositional data from source regions. In this paper, we: (1) present high-throughput LA-ICPMS analysis protocols needed to generate statistically meaningful detrital K-feldspar Pb isotope data sets; (2) develop an interpretative approach based upon 208Pb/206Pb vs. 207Pb/206Pb that incorporate information from the U- and Th-decay systems into one two-dimensional plot that is amenable to analysis using two-dimensional Kolmogorov–Smirnoff statistical tests; (3) generate new Pb isotopic data from basement rocks from southwestern North America to improve knowledge of the Pb isotopic properties of potential source regions; and (4) generate new Pb isotopic data from Lower Eocene to Lower Miocene sedimentary rocks to evaluate changes in drainage patterns that occurred in response to deformation that affected the southern California margin. Through this case study, we demonstrate how our new analytical and interpretative methods could be profitably applied to future geochemical and provenance studies and tectonically driven re-organization of drainage patterns.

Modeling elk‐to‐livestock transmission risk to predict hotspots of brucellosis spillover

Released March 14, 2019 16:27 EST

2019, Journal of Wildlife Management

Nathaniel D. Rayl, Kelly M. Proffitt, Emily S. Almberg, Jennifer D. Jones, Jerod A. Merkle, Justin A. Gude, Paul C. Cross

Wildlife reservoirs of infectious disease are a major source of human‐wildlife conflict because of the risk of potential spillover associated with commingling of wildlife and livestock. In the Greater Yellowstone Ecosystem, the presence of brucellosis (Brucella abortus) in free‐ranging elk (Cervus canadensis) populations is of significant management concern because of the risk of disease transmission from elk to livestock. We identified how spillover risk changes through space and time by developing resource selection functions using telemetry data from 223 female elk to predict the relative probability of female elk occurrence daily during the transmission risk period. We combined these spatiotemporal predictions with elk seroprevalence, demography, and transmission timing data to identify when and where abortions (the primary transmission route of brucellosis) were most likely to occur. Additionally, we integrated our predictions of transmission risk with spatiotemporal data on areas of potential livestock use to estimate the daily risk to livestock. We predicted that approximately half of the transmission risk occurred on areas where livestock may be present (i.e., private property or grazing allotments). Of the transmission risk that occurred in livestock areas, 98% of it was on private ranchlands as opposed to state or federal grazing allotments. Disease prevalence, transmission timing, host abundance, and host distribution were all important factors in determining the potential for spillover risk. Our fine‐resolution (250‐m spatial, 1‐day temporal), large‐scale (17,732 km2) predictions of potential elk‐to‐livestock transmission risk provide wildlife and livestock managers with a useful tool to identify higher risk areas in space and time and proactively focus actions in these areas to separate elk and livestock to reduce spillover risk.

Climate, streamflow, and lake-level trends in the Great Lakes Basin of the United States and Canada, water years 1960–2015

Released March 14, 2019 16:15 EST

2019, Scientific Investigations Report 2019-5003

Parker A. Norton, Daniel G. Driscoll, Janet M. Carter

Water levels in the Great Lakes fluctuate substantially because of complex interactions among inputs (precipitation and streamflow), outputs (evaporation and outflow), and other factors. This report by the U.S. Geological Survey in cooperation with the Great Lakes Restoration Initiative was completed to describe trends in climate, streamflow, lake levels, and major water-budget components within the Great Lakes Basin for water years (WYs) 1960–2015 (study period). Resulting trends are applicable only to the study period and should not be considered indicative of longer-term trends.

Analyses of climate trends used monthly data from the Parameter-elevation Regressions on Independent Slopes Model, which are available only for the United States. Trend tests were completed for annual and seasonal time series of monthly means for total precipitation, daily minimum air temperature (Tmin), and daily maximum air temperature (Tmax). Statistical significance for all time-trend tests (climate, streamflow, and lake levels) was determined using the Mann‑Kendall test for probability values less than or equal to 0.10. Trend analyses were completed without adjustments for serial correlation; however, a modified Mann-Kendall test was subsequently used to examine potential effects of short-term persistence in time-series data. Effects of short-term persistence were considered inconsequential for climate data and minor for streamflow data; however, the presence of short-term persistence in water-budget components had more substantial effects on trend analyses.

Spatial distributions of trends in climatic data for WYs 1960–2015 for the U.S. part of the Great Lakes Basin (land only) indicate (1) generally ubiquitous upward trends in Tmin and (2) a sharp transition from neutral or downward trends in precipitation northwest of Lake Michigan to generally upward trends east of Lake Michigan. Trends in Tmax were not statistically significant. Analyses of annual climatic data aggregated for the U.S. land part of the Great Lakes Basin indicated statistically significant upward trends for precipitation and Tmin, and similar statistically significant trends existed for all the individual lake subbasins except Lake Superior.

Of 103 U.S. Geological Survey streamgages analyzed for streamflow trends, 71 had significant annual trends (54 upward and 17 downward). Downward trends in annual streamflow are concentrated northwest of Lake Michigan (16 streamgages), and upward trends are concentrated east of Lake Michigan (53 streamgages). Of the 71 streamgages with significant annual trends, 70 had at least one season with a significant trend that matched the annual trend direction.

Of 35 Environment and Climate Change Canada streamgages analyzed, 22 had significant upward trends in annual streamflow, and all but 1 of these 22 had at least one season with a significant upward trend. None of the Environment and Climate Change Canada streamgages had significant downward annual trends, and only one had a significant downward seasonal trend.

Trends in lake levels and several major water-budget components affecting lake levels were analyzed for the study period. Significant downward trends in lake level and outflow for Lake Superior are driven primarily by low lake levels and outflows during WYs 1998–2014. A significant downward trend in runoff from the contributing drainage area also is indicated, which is consistent with numerous streamgages northwest of Lake Michigan with significant downward trends in annual streamflow. A significant upward trend in annual overlake evaporation also is indicated, which is consistent with the spatially distributed upward trends in annual Tmin.

The sum of overlake precipitation and runoff from the contributing drainage area for each of the Great Lakes, less overlake evaporation, composes a variable called net basin supply (NBS). A significant downward trend in NBS is indicated for Lake Superior, which is consistent with significant trends for individual components of runoff (downward) and evaporation (upward) that contributed to a significant downward trend for lake outflow. Statistically significant upward trends in NBS for Lake Saint Clair and Lake Ontario offset the downward trend for Lake Superior and combine with nonsignificant upward trends in NBS for Lakes Michigan and Huron and Lake Erie to produce a neutral trend in NBS for the basin.

A predictable pattern in monthly mean lake levels is noted for Lake Superior, with the minimum for each year usually during or near March and the maximum commonly during or near September or October. When an October lake level is in a period of substantial decline, potential for an ensuing short-term period of below-mean lake levels is enhanced. Downstream from Lake Superior, monthly lake levels have sawtooth patterns that somewhat resemble those for Lake Superior but with decreased predictability in timing.

Similar to Lake Superior, Lakes Michigan and Huron, Lake Saint Clair, and Lake Erie all have a prolonged period of low lake levels around WYs 1998–2014; however, a significant downward trend is indicated only for Lakes Michigan and Huron. All these lakes also have a period of low lake levels before about WY 1968, when minimum lake levels were lower than during WYs 1998–2014. The significant downward trend of outflow from Lake Superior is carried downstream into Lakes Michigan and Huron; however, trends in outflow from the next three lakes downstream (Lakes Saint Clair, Erie, and Ontario) are offset by increased precipitation and runoff and are not significant.

Constraining the oxygen isotopic composition of nitrate produced by nitrification

Released March 14, 2019 15:37 EST

2019, Environmental Science & Technology (53) 1206-1216

Danielle S. Boshers, Julie Granger, Craig R. Tobias, John K. Böhlke, Richard L. Smith

Measurements of the stable isotope ratios of nitrogen (15N/14N) and oxygen (18O/16O) in nitrate (NO3) enable identification of sources, dispersal, and fate of natural and contaminant NO3 in aquatic environments. The 18O/16O of NO3 produced by nitrification is often assumed to reflect the proportional contribution of oxygen atom sources, water, and molecular oxygen, in a 2:1 ratio. Culture and seawater incubations, however, indicate oxygen isotopic equilibration between nitrite (NO2) and water, and kinetic isotope effects for oxygen atom incorporation, which modulate the NO3 18O/16O produced during nitrification. To investigate the influence of kinetic and equilibrium effects on the isotopic composition of NO3 produced from the nitrification of ammonia (NH3), we incubated streamwater supplemented with ammonium (NH4+) and increments of 18O-enriched water. Resulting NO3 18O/16O ratios showed (1) a disproportionate sensitivity to the 18O/16O ratio of water, mediated by isotopic equilibration between water and NO2, as well as (2) kinetic isotope discrimination during O atom incorporation from molecular oxygen and water. Empirically, the NO3 18O/16O ratios thus produced fortuitously converge near the 18O/16O ratio of water. More elevated NO3 18O/16O values commonly reported in soils and oxic groundwater may thus derive from processes additional to nitrification, including NO3 reduction.

Focus areas for data acquisition for potential domestic sources of critical minerals—Rare earth elements

Released March 14, 2019 15:15 EST

2019, Open-File Report 2019-1023-A

Jane M. Hammarstrom, Connie L. Dicken

Rare earth elements (REEs) are critical mineral commodities for the United States. In response to a need for information on potential domestic sources of REEs in mineral deposits, the U.S. Geological Survey (USGS) identified broad focus areas throughout the conterminous United States and Alaska as a guide for selecting new geoscience research areas. This study was done to support the USGS Earth Mapping Resources Initiative (Earth MRI).

Focus areas are identified in four regions of the United States (Alaska, West, Central, and East) by mineral deposit type. The areas are described in a companion USGS data release that consists of a map in a geographic information system and accompanying tables that document the rationale for each focus area (C.L. Dicken and others, 2019, https://doi.org/10.5066/P95CHIL0). This open-file report describes the methodology that was used to identify focus areas and determine new data acquisition needs. Deposit types that are likely to be of interest for future exploration and development of domestic nonfuel REE resources include deposits associated with carbonatites and peralkaline rocks, iron oxide-apatite deposits, monazite-bearing placers, and REE-enriched phosphorites.

Geomorphic survey of North Fork Eagle Creek, New Mexico, 2017

Released March 14, 2019 13:05 EST

2019, Open-File Report 2018-1187

Alexander P. Graziano

About one-quarter of the water supply for the Village of Ruidoso, New Mexico, is derived from groundwater pumping along North Fork Eagle Creek in the Eagle Creek Basin near Alto, New Mexico. Because of concerns regarding the effects of groundwater pumping on surface-water hydrology in the Eagle Creek Basin and the effects of the 2012 Little Bear Fire, which resulted in substantial losses of vegetation in the basin, the monitoring of North Fork Eagle Creek for short-term geomorphic change has been required by the U.S. Department of Agriculture Forest Service, Lincoln National Forest, as part of the permitting decision that allows for the continued pumping of the production wells. The monitoring of short-term geomorphic change in North Fork Eagle Creek began in June 2017 with a geomorphic survey of the stream reach located between the North Fork Eagle Creek near Alto, New Mexico, streamflow-gaging station (USGS site 08387550) and the Eagle Creek below South Fork near Alto, New Mexico, streamflow-gaging station (USGS site 08387600). The 2017 geomorphic survey was conducted by the U.S. Geological Survey (USGS), in cooperation with the Village of Ruidoso, and was the first in a planned series of five annual geomorphic surveys. The results of the 2017 geomorphic survey are summarized and interpreted in this report and are provided in their entirety in its companion data release.

The study reach is 1.86 miles long, and large sections of the reach are characterized by intermittent streamflow. Where water is normally present (including at the upper and lower portions of the reach near the streamflow-gaging stations), the discharge typically remains below 2 cubic feet per second throughout the year. Therefore, if geomorphic change is to occur, it will likely be driven by seasonal high-flow events. Discharge records from streamflow-gaging stations in the Eagle Creek Basin indicated that high-flow events in the basin (with peaks above 50 cubic feet per second) typically occurred during the North American monsoon months of July, August, and September. Additionally, the records appear to indicate that, as expected, overland runoff and “flashy” responses to rainfall have increased in the 5 years since the 2012 Little Bear Fire.

For the 2017 geomorphic survey of North Fork Eagle Creek, cross sections were established and surveyed at 14 locations along the study reach. Cross-section survey results indicated that channel characteristics (including channel width and area) varied widely along the study reach. Also, as part of the survey, woody debris accumulations and pools in the channel of the study reach were identified, cataloged, photographed, and surveyed for location. There were 58 woody debris accumulations and 14 pools found in the study reach. On the basis that debris jams could be a driver of geomorphic change in North Fork Eagle Creek, woody debris accumulations were classified according to their debris jam potential. The burn marks found on some woody debris indicated that the 2012 Little Bear Fire may be a contributing factor to the volume of debris in North Fork Eagle Creek. However, the woody debris present at the time of the survey did not appear to have substantially affected the geomorphic state of the study reach. Further, the structure and composition of the woody debris accumulations indicated that, under high-flow conditions, most woody debris would likely be transported downstream and out of the study reach without causing substantial geomorphic change through further jamming.

Effect of size-biased sampling on resource predictions from the three-part method for quantitative mineral resource assessment—A case study of the gold mines in the Timmins-Kirkland Lake area of the Abitibi greenstone belt, Canada:

Released March 14, 2019 11:45 EST

2019, Scientific Investigations Report 2018-5149

Karl J. Ellefsen

The three-part method for quantitative mineral resource assessment is used by the U.S. Geological Survey to predict, within a specified assessment area, the number of undiscovered mineral deposits and the quantity of mineral resources in those undiscovered deposits. The effects of size-biased sampling on such predictions are evaluated in a case study that involves gold mines from the Timmins-Kirkland Lake area of the Abitibi greenstone belt, Canada. The gold mines are divided, based upon the time of the assessment, into two groups: existing mines and future mines. The total produced gold for the existing mines are used to predict, with the three-part method, the total produced gold for the future mines. Then the predictions are compared to the known, total produced gold for the future mines. For comparisons using the mean, the predictions are 1.6 to 12 times too high, depending upon the time of the assessment and the probability density function characterizing the total produced gold in the existing mines. For comparisons using the median, the predictions are 1.3 to 10 times too high, depending upon the time of the assessment. The reason for these excessively high predictions is that the three-part method is based on the assumption that the total produced gold from the existing mines is representative of the total produced gold in the future mines; this assumption is inappropriate because of size-biased sampling. There is reason to be concerned that size-biased sampling adversely affected the resource predictions of previous U.S. Geological Survey assessments that were conducted with the three-part method.

Groundwater and surface-water data collection for Mason County, western Washington, 2016–18

Released March 14, 2019 10:55 EST

2019, Data Series 1106

Alison E. Tecca, Lonna M. Frans

Groundwater levels and surface water flow measurements were collected from August 2016 to September 2018 to provide the Mason Conservation District and other stakeholders with basic knowledge of existing water resources in Mason County, Washington. Additionally, the data were collected with the intent of contributing to informed decision making about groundwater use, management, and conservation throughout the county and for future inclusion in a groundwater model. Data were collected and compiled for 130 sites—110 wells and 20 miscellaneous surface-water discharge sites. In the spring of 2016, field reconnaissance was conducted to locate suitable locations for baseflow discharge measurements to be used for estimating groundwater contribution to surface flow. In the summer of 2016, a field inventory of wells was conducted to acquire locational data and to assess the suitability of the wells for inclusion in a monthly groundwater-level monitoring network. Groundwater levels were measured bimonthly in the 64 wells over 2 years. Streamflow measurements were conducted two times each summer during two summers for each of the 20 surface water sites.

Stream sediment geochemistry of four small drainages on the north shore of Kauai west of Hanalei

Released March 14, 2019 10:26 EST

2019, Open-File Report 2019-1007

Renee K. Takesue, Curt D. Storlazzi

Geochemical compositions of fine-grained stream sediment from four drainages on the north shore of the island of Kauai, Hawaii, west of Hanalei and two back-beach sites were explored to increase understanding about land-based runoff and ecological risk from runoff to nearshore coral communities. Stream and beach sediment were collected between July 30 and August 2, 2016, and major, minor, and trace elements in the less than 63 micrometer-diameter fraction were analyzed by inductively coupled plasma optical emission spectroscopy and mass spectroscopy. The potentially toxic metals Cr, Cu, Ni, and Zn exceeded levels at which adverse biological effects could be observed; however, these metals seemed to be largely mineral-bound and thus were unlikely to harm organisms. Cd and Pb were below levels of ecological concern. Only a small amount of fine-grained sediment was retained on beaches west of Hanalei sampled in summer 2016 (mean=8.8 percent, median=0.4 percent, range=0–92.8 percent, n=41). Although the scarcity of fine-grained sediment precluded land-based runoff sourcing to the nearshore region, it did indicate that fine-grained sediment and associated contaminants did not accumulate over the long term in the sampled intertidal, subtidal, and reef-flat environments, which would reduce sediment-related pressures on coral communities there.

Abundance and productivity of marbled murrelets (Brachyramphus marmoratus) off central California during the 2018 breeding season

Released March 14, 2019 10:05 EST

2019, Data Series 1107

Jonathan J. Felis, Emily C. Kelsey, Josh Adams

Executive Summary

Marbled murrelets (Brachyramphus marmoratus) have been listed as “endangered” by the State of California and “threatened” by the U.S. Fish and Wildlife Service since 1992 in California, Oregon, and Washington. Information regarding marbled murrelet abundance, distribution, population trends, and habitat associations is critical for risk assessment, effective management, evaluation of conservation efficacy, and ultimately, to meet Federal- and State-mandated recovery efforts for this species. During June–August 2018, the U.S. Geological Survey Western Ecological Research Center continued previously established, long-term (1999–2018), at-sea surveys to estimate abundance and productivity of marbled murrelets in U.S. Fish and Wildlife Service Conservation Zone 6 (San Francisco Bay to Point Sur in central California). Using conventional distance sampling methods, we estimated marbled murrelet abundance using 137 detections of 227 individuals observed on 9 surveys. The abundance estimated for the entire study area using all surveys in 2018 was 370 birds (95-percent confidence interval, 250–546 birds). Estimated abundance from 2018 is comparable to most prior years of study, except for 2001–03, when greater abundances were estimated. In 2018, we estimated reproductive productivity (calculated as the hatch-year [HY] to after-hatch-year [AHY] ratio) using four detections of four HY individuals observed on six surveys. After date-correcting HY and AHY counts to account for birds expected to be absent from the water while inland at nests, the date-corrected juvenile ratio was 0.047 ± 0.024 standard error. We updated a synthesized database of all Zone 6 marbled murrelet survey data since 1999 with 2018 data to allow scientists and managers to evaluate established survey methods and assess trends in abundance and productivity estimates.

Least Bell’s Vireo (Vireo bellii pusillus) and Southwestern Willow Flycatcher (Empidonax traillii extimus) surveys in the Sepulveda Dam Basin, Los Angeles County, California—2018 data summary

Released March 14, 2019 09:38 EST

2019, Data Series 1105

Ryan E. Pottinger, Barbara E. Kus

Executive Summary

We surveyed for Least Bell’s Vireos (Vireo bellii pusillus; vireo) and Southwestern Willow Flycatchers (Empidonax traillii extimus; flycatcher) in cooperation with the U.S. Army Corps of Engineers along Bull Creek, Haskell Creek, and the Los Angeles River (Sepulveda Dam project area) in Los Angeles County, California, in 2018. Four vireo surveys were conducted between April 27 and July 18, 2018, and three flycatcher surveys were conducted between May 24 and July 18, 2018. We found 14 territorial male vireos, 7 of which were confirmed as paired. Sixty-four percent of vireos were detected along the Los Angeles River, 21 percent along Haskell Creek, and 14 percent along Bull Creek. Eighty-six percent of vireos were detected in habitat characterized as mixed willow, and all vireos were detected in habitat with greater than 50 percent native plant cover. No flycatchers were observed in the survey area in 2018.

North American Commission on Stratigraphic Nomenclature Note 69 – Application for addition of subseries/subepoch to the North American Stratigraphic Code

Released March 13, 2019 15:48 EST

2019, Stratigraphy (15) 261-263

Marie-Pierre Aubry, Richard H. Fluegeman, Lucy E. Edwards, Brian R. Pratt, Carlton E. Brett

Consistency in stratigraphic nomenclature enables communication among scientists both regionally and globally, thus requiring the North American Stratigraphic Code, as presented by the North American Commission on Stratigraphic Nomenclature, to follow international convention. The ratification of three subseries of the Holocene by the InternationalUnion of Geological Sciences (IUGS) in June 2018 warrants the integration of subseries among formal chronostratigraphic ranks in the Code. The purpose ofmaking subseries a formal rank is that it aligns the Code with the International StratigraphicGuide, and establishes the option of using the prefixes super- and sub- for other chronostratigraphic and geochronologic ranks. This is in accordance with the guiding principle of the Code to make it as consistent as possible with international usage and to foster innovations to meet the expanding and changing needs of earth scientists.

Improved enrichment factor calculations through principal component analysis: Examples from soils near breccia pipe uranium mines, Arizona, USA

Released March 13, 2019 15:20 EST

2019, Environmental Pollution (248) 90-100

Carleton R. Bern, Katie Walton-Day, David L. Naftz

The enrichment factor (EF) is a widely used metric for determining how much the presence of an element in a sampling media has increased relative to average natural abundance because of human activity. Calculation of an EF requires the selection of both a background composition and a reference element, choices that can strongly influence the result of the calculation. Here, it is shown how carefully applied, classical principal component analysis (PCA) examined via biplots can guide the selections of background compositions and reference elements. Elemental data were treated using the centered log ratio (CLR) transformation, and multiple subsets of major and trace elements were examined to gain different perspectives. The methodology was applied to a dataset of elemental soil concentrations from around breccia pipe uranium mines in Arizona, U.S.A., with most samples collected via incremental sampling methodology. Storage of ore at the surface creates the potential for wind dispersal of ore-derived material. Uranium was found to be the best individual tracer of dispersal of ore-derived material to nearby soils, with EF values up to 75. Sulfur, As, Mo, and Cu were also enriched but to lesser degrees. The results demonstrate several practical benefits of a PCA in these situations: (1) the ability to identify one or more elements best suited to distinguish a specific source of enrichment from background composition; (2) understanding how background compositions vary within and between sites; (3) identification of samples containing enriched or anthropogenic materials based upon their integrated, multi-element composition. Calculating the most representative EF values is useful for numerical assessment of enrichment, whether anthropogenic or natural. As shown here, however, the PCA and biplot method provide a visual approach that integrates information from all elements for a given subset of data in a manner that yields geochemical insights beyond the power of the EF.

Assessment of skin and liver neoplasms in white sucker (Catostomus commersonii) collected in the Sheboygan River Area of Concern, Wisconsin, in 2017

Released March 13, 2019 14:00 EST

2019, Open-File Report 2019-1014

Vicki S. Blazer, Heather L. Walsh, Ryan P. Braham, Patricia M. Mazik

Two hundred adult white sucker (Catostomus commersonii), age 3 years and older, were collected from the lower Sheboygan River Area of Concern in 2017, during the spring spawning run. Fish were euthanized, weighed, and measured, and any visible abnormalities were documented. Pieces of raised skin lesions as well as five to eight pieces of liver were removed and preserved for histopathological analyses. Skin and liver neoplasm prevalence was determined for assessment of the Fish Tumors or Other Deformities Beneficial Use Impairment. Although 45.5 percent of the suckers had raised skin lesions, the prevalence of skin neoplasms, either papilloma or squamous cell carcinoma, was 29.5 percent. This observation was similar to the prevalence (32.6 percent) of skin neoplasms in 2012; however, the percentage of squamous cell carcinoma was higher in 2017 (9.5 percent) than in 2012 (2.1 percent). The prevalence of liver neoplasms in 2017 (8.5 percent) was similar to that in 2012 (8.3 percent).

Flood-inundation maps for the Yellow River from River Drive to Centerville Highway, Gwinnett County, Georgia

Released March 13, 2019 09:00 EST

2019, Scientific Investigations Report 2019-5009

Jonathan W. Musser

Digital flood-inundation maps for a 16.4-mile reach of the Yellow River in Gwinnett County, Georgia, from 0.5 mile upstream from River Drive to Centerville Highway (Georgia State Route 124) were developed to depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at two U.S. Geological Survey (USGS) streamgages in the mapped area. The maps for the 9.0-mile reach from 0.5 mile upstream from River Drive to Stone Mountain Highway (U.S. Route 78) are referenced to the streamgage Yellow River near Snellville, Ga. (station 02206500), and the maps for the 7.4-mile reach from Stone Mountain Highway to Centerville Highway are referenced to the streamgage Yellow River at Ga. 124, near Lithonia, Ga. (02207120). Real-time stage information from these streamgages can be used with these maps to estimate near real-time areas of inundation. The forecasted peak-stage information for the USGS streamgages Yellow River near Snellville, Ga. (02206500), and Yellow River at Ga. 124, near Lithonia, Ga. (02207120), can be used in conjunction with the maps developed for this study to show predicted areas of flood inundation.

A one-dimensional step-backwater model was developed using the U.S. Army Corps of Engineers Hydrologic Engineering Center's River Analysis System (HEC–RAS) software for the Yellow River and was used to compute flood profiles for a 16.4-mile reach of the Yellow River. The hydraulic model was then used to simulate 16 water-surface profiles at 1.0-foot (ft) intervals at the Yellow River near Snellville streamgage and 17 water-surface profiles at 1.0-ft intervals at the Yellow River near Lithonia streamgage. At the Yellow River near Snellville streamgage, the profiles ranged from a stage of 18.0 ft, which is 819.1 ft above the North American Vertical Datum of 1988 (NAVD 88), to a stage of 33.0 ft, which is 834.1 ft above NAVD 88. At the Yellow River near Lithonia streamgage, the profiles ranged from the National Weather Service action stage of 13.0 ft, which is 732.5 ft above NAVD 88, to a stage of 29.0 ft, which is 748.5 ft above NAVD 88. The simulated water-surface profiles were then combined with a geographic information system digital elevation model—derived from light detection and ranging (lidar) data having a 5.0-ft horizontal resolution—to delineate the area flooded at each 1.0-ft interval of stream stage for both streamgages.

Harmful algal blooms

Released March 13, 2019 09:00 EST

2019, General Information Product 188

U.S. Geological Survey

This postcard provides details about "Cyanobacterial Harmful Algal Blooms and U.S. Geological Survey Science Capabilities, "Open File Report 2016-1174, where you can find details about how U.S. Geological Survey (USGS) scientists use traditional methods and emerging technologies in collaboration with numerous partners to lead a diverse range of studies addressing harmful algal bloom (HAB) issues in water bodies throughout the United States. Cutting-edge USGS research in HABs has advanced scientific understanding and led to practical applications that help protect ecological and human health.

Assessment of undiscovered oil and gas resources in the Tindouf Basin Province, North Africa, 2018

Released March 12, 2019 17:00 EST

2019, Fact Sheet 2019-3006

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

Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean resources of 2.6 billion barrels of oil and 123.9 trillion cubic feet of gas in the Tindouf Basin Province of North Africa.

Fall Chinook salmon (Oncorhynchus tshawytscha), sand roller (Percopsis transmontana), and smallmouth bass (Micropterus dolomieu) interactions in a Snake River reservoir: A tale of three species

Released March 12, 2019 16:20 EST

2019, Northwestern Naturalist (100) 26-36

Rulon J. Hemingway, Kenneth F. Tiffan, John M. Erhardt, Tobyn N. Rhodes, Brad K. Bickford

We studied some of the relationships between federally listed fall Chinook Salmon, Oncorhynchus tshawytscha, endemic Sand Roller, Percopsis transmontana, and non-native Smallmouth Bass, Micropterus dolomieu, in Lower Granite Reservoir on the Snake River. Because of its recent reappearance and population increase, the Sand Rollers could be filling the role of a “native invader” in the reservoir food web. We speculated that Sand Rollers could either negatively affect fall Chinook Salmon by potentially competing with them for resources in shoreline habitats or, alternatively, benefit the salmon by providing a buffer against Smallmouth Bass predation. Nighttime beach seining showed that habitat use by fall Chinook Salmon and Sand Rollers overlapped completely in spring when both species were present along shorelines. Diet data from stomach samples also showed high overlap, but data on stable isotopes of 13C and 15N suggested that each species could be obtaining much of their dietary energy from different reservoir locations. Although habitat and diet overlap are evidence of competition, diel and spatial partitioning of resource use between fall Chinook Salmon and Sand Rollers may act to reduce potential competition. Analyses of Smallmouth Bass diets showed that fall Chinook Salmon and Sand Rollers comprised the majority of prey fish consumed by bass. Across years, as Smallmouth Bass increased their consumption of Sand Rollers (range 0.219 to 0.392 fish smallmouth-1 day-1), they decreased their consumption of fall Chinook Salmon (range 0.114 to 0.050 fish smallmouth-1 day-1). The greatest effect Sand Rollers may have on fall Chinook Salmon in Lower Granite Reservoir is to serve as a buffer against Smallmouth Bass predation.

Contemporary environmental assessment using a viability analysis in a large river system to inform restoration and adaptive management decisions

Released March 12, 2019 15:18 EST

2019, Scientific Investigations Report 2019-5002

Robin L. DeBruyne, Edward F. Roseman, Jason E. Ross, Kurt R. Newman, Russell M. Strach

As large-scale restoration plans for degraded aquatic habitats evolve, it is essential that multiorganizational collaborations have a common vision to achieve consensus on restoration goals. Development of restoration targets and postrestoration monitoring strategies can be focused using a viability analysis framework that supports an adaptive management process. Viability analysis is a robust and accommodating framework, adaptable to any restoration monitoring program and, through the determination of common desired endpoints, can aid consensus building and collaboration across jurisdictional boundaries. In the St. Clair-Detroit River System, which is the Great Lakes connecting channel between southern Lake Huron and western Lake Erie, a viability analysis framework was used to evaluate environmental parameters associated with fisheries and aquatic restoration efforts and to gauge the overall health of the aquatic environment. Steps to derive the viability analysis were as follows: (1) establishing meaningful baseline metrics, (2) identifying information deficiencies, and (3) placing the context of current conditions into a usable format for managers and practitioners. Most geographic segments were designated in overall fair condition, and the conservation targets were designated in either good or fair condition, based on available assessed indicators. Many indicators were unable to be assessed or assigned condition status, which identified research and monitoring data gaps. Metrics associated with native migratory fishes, Lake St. Clair, and islands are generally in better condition than metrics associated with the coastal terrestrial systems, aerial migrants, and coastal wetlands. These results were not unexpected given the highly urbanized landscape of the St. Clair-Detroit River System. Resource managers in the corridor can use these results to identify knowledge gaps, research and restoration priorities, and to assess progress towards meeting restoration goals.

Geochemistry of a thermally immature Eagle Ford Group drill core in central Texas

Released March 12, 2019 10:29 EST

2019, Organic Geochemistry

Katherine L. French, Justin E. Birdwell, Katherine J. Whidden

The Upper Cretaceous Eagle Ford Group displays significant lateral and vertical geochemical variability. Much of the work on the Eagle Ford Group has been focused southwest of the San Marcos arch. To more fully characterize the Eagle Ford across the entire region, a thermally immature drill core was acquired north of the San Marcos arch that recovered the Pepper Shale and the Eagle Ford Group. Molecular and isotopic analyses of rock extracts were combined with bulk organic and inorganic geochemistry and mineralogy to track the variability in organic matter source and depositional environment, as well as to identify drivers of organic enrichment.

The Pepper Shale received significant terrigenous organic matter in its distal deltaic or prodeltaic setting compared to the more distally deposited Eagle Ford Group that primarily hosts marine organic matter. The upper Eagle Ford contains two chemofacies. The older upper Eagle Ford chemofacies has similar mineralogy and organic matter to the underlying lower Eagle Ford, and both intervals display good to excellent source rock potential. In contrast, the younger upper Eagle Ford chemofacies has a different sterane assemblage, a larger terrigenous component, and a higher clay mineral abundance. However, anoxic to euxinic depositional conditions distinguish the lower Eagle Ford from the upper Eagle Ford, which was deposited under oxic to dysoxic conditions. Redox chemistry and organic matter source are two important variables that determine source rock quality, but they did not change in parallel during Eagle Ford deposition. Differences in organic facies explain the Tmax variability, and depositional redox conditions governed organic-richness in the Eagle Ford Group in central Texas.

Towards determining spatial methane distribution on Arctic permafrost bluffs with an unmanned aerial system

Released March 12, 2019 10:23 EST

2019, SN Applied Sciences (1) 1-9

Ferdinand K. J. Oberle, Ann E. Gibbs, Bruce M. Richmond, Li H. Erikson, Mark P. Waldrop, Peter W. Swarzenski

Arctic permafrost stores vast amounts of methane (CH4) in subsurface reservoirs. Thawing permafrost creates areas for this potent greenhouse gas to be released to the atmosphere. Identifying ‘hot spots’ of methane flux on a local scale has been limited by the spatial scales of traditional ground-based or satellite-based methane-sampling methods. Here we present a reliable and an easily replicable design using only off-the-shelf, cost-effective methane sensor components and an Unmanned Aerial System (UAS). Our results demonstrate the high efficiency of the design and the advantages of this methodology for environmental methane studies that are subjected to the high spatial variability of methane levels. On Barter Island, NE Alaska, we noted spikes in CH4 concentrations coincident with topographic features or anomalies. Such spikes may be attributed to enhanced land/air transfer and may reveal zones of high methane production and/or minimal oxidation in areas of thermoerosional gullies along thawing coastal zones. Thermoerosional gullies represent hotspots that release significantly higher levels of methane than the surrounding areas, thus suggesting that point sampling is inadequate in characterizing methane releases and that increasing rates of permafrost thaw may result in increasing point sources of high CH4 emissions.

Long‐term plant community trajectories suggest divergent responses of native and non‐native perennials and annuals to vegetation removal and seeding treatments

Released March 12, 2019 10:19 EST

2019, Restoration Ecology

Stella M. Copeland, Seth M. Munson, John B. Bradford, Bradley J. Butterfield, Kevin L. Gunnell

Land managers frequently apply vegetation removal and seeding treatments to restore ecosystem function following woody plant encroachment, invasive species spread, and wildfire. However, the long‐term outcome of these treatments is unclear due to a lack of widespread monitoring. We quantified how vegetation removal (via wildfire or management) with or without seeding and environmental conditions related to plant community composition change over time in 491 sites across the intermountain western United States. Most community metrics took over 10 years to reach baseline conditions posttreatment, with the slowest recovery observed for native perennial cover. Total cover was initially higher in sites with seeding after vegetation removal than sites with vegetation removal alone, but increased faster in sites with vegetation removal only. Seeding after vegetation removal was associated with rapidly increasing non‐native perennial cover and decreasing non‐native annual cover. Native perennial cover increased in vegetation removal sites irrespective of seeding and was suppressed by increasing non‐native perennial cover. Seeding was associated with higher non‐native richness across the monitoring period as well as initially higher, then declining, total and native species richness. Several cover and richness recovery metrics were positively associated with mean annual precipitation and negatively associated with mean annual temperature, whereas relationships with weather extremes depended on the lag time and season. Our results suggest that key plant groups, such as native perennials and non‐native annuals, respond to restoration treatments at divergent timescales and with different sensitivities to climate and weather variation.

Diversity and abundance of wild bees in an agriculturally dominated landscape of eastern Colorado

Released March 12, 2019 10:17 EST

2019, Journal of Insect Conservation (23) 187-197

H. S. Arathi, Mark W. Vandever, Brian S. Cade

Agricultural intensification has resulted in loss of natural and semi-natural habitats impacting several important ecosystem services. One group of organisms that has suffered greatly are the bees and hence pollination, the supporting ecosystem service they complete. The United States Department of Agriculture (USDA) Conservation Reserve Program (CRP) has implemented conservation practices designed to improve habitat for pollinators in agroecosystems by paying to recover environmentally sensitive agricultural land from production, and restoring them by planting native grass mixes, pollinator-friendly legumes and wildflowers. Our study, aimed at demonstrating the efficacy of this practice, measured diversity and abundance of wild bee genera in the agricultural landscape of eastern semiarid regions of Colorado, USA, where CRP practices were implemented. Over our 3-year study, we obtained a total of 16,207 bees belonging to 51 genera. We found inconsistent differences in number of bee genera and abundance of bees in CRP fields supplemented with wildflowers compared to those with conventional grass seed mix. However, we observed only a 40–80% overlap in bee genera between fields supplemented with wildflowers and those with grass seed mixes indicating that diversity was enhanced by having both habitats. With the caveat that 3 years is a very short period to see appreciable changes, our results suggest that recovering environmentally sensitive land can strengthen pollinator populations in landscapes dominated by agricultural activities. In addition, periodic evaluation and maintenance of these recovered lands will further support the efforts towards revitalization of ecosystem services in these areas.

Effects of land use on greenhouse gas flux in playa wetlands and associated watersheds in the High Plains, USA

Released March 11, 2019 14:49 EST

2019, Agricultural Sciences (10) 181-201

Dale W. Daniel, Loren M. Smith, Scott T. McMurry, Brian A. Tangen, Charles F. Dahl, Ned Euliss, Ted LaGrange

In the High Plains, U.S., native prairie conversion to cropland agriculture has resulted in a loss of service delivery capabilities from most depressional wetlands as a result of sedimentation. Restoring historic hydrological conditions to affected wetlands may rejuvenate some services, however, there may be tradeoffs due to emissions of CH4 and N2O. We evaluated the influence of two predominant conservation programs (Wetlands Reserve Program, WRP and Conservation Reserve Program, CRP) on gas emissions (CO2, CH4, N2O) from 42 playas and uplands in the High Plains of Nebraska. Because playa restoration through the WRP is most prevalent in the Rainwater Basin (RWB), we studied 27 playas/uplands among reference condition, cropland, and WRP land uses. We studied 15 playas/uplands within native grassland, cropland, and CRP land uses in the Western High Plains (WHP) of Nebraska. Emissions were collected bi-weekly from April-October of 2012 and 2013 from four landscape positions extending outward from the wetland center into upland. In RWB playas, CH4 and N2O emissions were similar among land uses but CO2 was 28% higher in cropland than WRP wetlands. Cropland uplands emitted 648% more N2O than reference and WRP uplands. Overall, net CO2-equiv emissions were lower in playas/uplands in WRP, suggesting that benefits of playa restoration may include climate mitigation services as well as increased water storage capacity and biodiversity provisioning. In the WHP, cropland and grassland playas emitted 46 and 23 times more CH4, respectively, than CRP in 2013. Playas in CRP emitted 43% less N2O than cropland playas. In 2013, net emissions for cropland and native grassland playas were 75% and 39% greater, respectively, than CRP playas. In the WHP, the benefits of lower gas emissions must be appropriately weighted against tradeoffs of ecosystem services related to shorter hydroperiods as a result of reduced runoff into playas in CRP.

Complete genome sequences of the index isolates of two genotypes of Pacific salmon paramyxovirus

Released March 11, 2019 14:46 EST

2019, Microbiology Resource Announcements (8) 1-2

James Winton, William N. Batts, Rachel L. Powers, Maureen K. Purcell

We report here the genome sequences of two index strains of Pacific salmon paramyxovirus isolated in 1982 and 1983 from adult salmon in Oregon. The isolates are most closely related to Atlantic salmon paramyxovirus, the type species of the genus Aquaparamyxovirus, but are sufficiently distinct to be considered two genotypes of a novel species.

Flood-inundation maps of the Meramec River from Eureka to Arnold, Missouri, 2018

Released March 11, 2019 13:38 EST

2019, Scientific Investigations Report 2019-5004

Benjamin J. Dietsch, Kellan R. Strauch

Libraries of digital flood-inundation maps that spanned a combined 37.2-mile reach of the Meramec River that extended upstream from Eureka, Missouri, to downstream near the confluence of the Meramec and Mississippi Rivers were created by the U.S. Geological Survey (USGS) in cooperation with the U.S. Army Corps of Engineers, Metropolitan St. Louis Sewer District, Missouri Department of Transportation, Missouri American Water, Federal Emergency Management Agency Region 7, and the cities of Pacific, Eureka, Wildwood, and Arnold. 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 cooperative USGS streamgages for the Meramec River near Eureka, Mo. (USGS station 07019000), the Meramec River at Valley Park, Mo. (USGS station 07019130), the Meramec River at Fenton, Mo. (USGS station 07019210), and the Meramec River at Arnold, Mo. (USGS station 07019300). Near-real-time stage data at these streamgages may be obtained from the USGS National Water Information System at https://doi.org/10.5066/F7P55KJN or the National Weather Service (NWS) Advanced Hydrologic Prediction Service at https://water.weather.gov/ahps/, which also forecasts flood hydrographs at these sites (listed as NWS sites erkm7, vllm7, fnnm7, and arnm7, respectively).

Flood profiles were computed for the stream reach by means of a calibrated one-dimensional step-backwater hydraulic model. The model was calibrated using a stage-discharge relation at the Meramec River near Eureka, Mo., streamgage (USGS station 07019000) and documented high-water marks from the flood of December 2015 through January 2016.

The calibrated hydraulic model was used to compute water-surface profiles: 1 set for the Meramec River near Eureka, Mo., streamgage (USGS station 07019000); 1 set for the Meramec River at Valley Park, Mo., streamgage (USGS station 07019130); 7 sets for the Meramec River at Fenton, Mo., streamgage (USGS station 07019210) for a range of Mississippi River conditions; and 8 sets for the Meramec River at Arnold, Mo., streamgage (USGS station 07019300) for a range of Mississippi River conditions. The water-surface profiles were produced for stages at 1-foot (ft) intervals referenced to the datum from each streamgage and ranging from the NWS action stage, or near bankfull discharge, to the stage corresponding to the estimated 0.2-percent annual exceedance probability (500-year recurrence interval) flood, as determined at the Meramec River near Eureka, Mo., streamgage (USGS station 07019000). The simulated water-surface profiles then were combined with a geographic information system digital elevation model (derived from light detection and ranging data having a 0.28-ft vertical accuracy and 3.28-ft horizontal resolution) to delineate the area flooded at each simulated 1-ft stage increment. Previously published flood-inundation maps were updated and incorporated in the flood map libraries for USGS stations 07019130 and 07019210 to complete the map sets corresponding to eight Mississippi River conditions.

The availability of these maps, along with internet information regarding current stage from the USGS streamgages 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 and for postflood recovery efforts.

Water-balance modeling of selected lakes for evaluating viability as long-term fisheries in Kidder, Logan, and Stutsman Counties, North Dakota

Released March 11, 2019 13:37 EST

2019, Scientific Investigations Report 2019-5007

Robert F. Lundgren, Benjamin C. York, Nathan A. Stroh, Aldo V. Vecchia

Water levels in lakes and wetlands in the central North Dakota Missouri Coteau region that were either dry or only sporadically held water since before the 1930s have been rising since the early 1990s in response to an extended wet period. The lakes have remained full since the mid-1990s, which has provided benefits to migratory waterfowl, fisheries, and wildlife. A small shift in climate conditions, either to drier or wetter conditions, can have a large effect on the lake levels of these water bodies. The North Dakota Game and Fish Department identified five lakes as candidates for sustaining long-term fisheries. The lakes are in Kidder, Stutsman, and Logan Counties, and some lakes might receive inflow from mostly freshwater aquifers, such as the Central Dakota and Streeter aquifers, and were mostly dry during the early 1990s. After about 1995, the lakes had filled up and were deep enough to sustain populations of game fish such as walleye, perch, and northern pike. Before investing in development of permanent fisheries and associated infrastructure, such as campgrounds and boat ramps, fisheries biologists needed to know if the lake levels are likely to remain high in coming decades.

The U.S. Geological Survey, in cooperation with the North Dakota Game and Fish Department, developed a water-balance model to determine the effects of precipitation, evapotranspiration, and groundwater interaction on lake volumes. The model was developed using climate input data and lake volumes for the calibration period 1992 through 2016, during which historical lake volumes could be estimated using land surface elevation data and Landsat images. Long-term (1940–2018) climate input data were used with the water-balance model to reconstruct historical lake volumes prior to the calibration period, and block-bootstrapping was used to simulate potential future climate input data and lake volumes for 2017 through 2067. The simulated future lake volumes were used to estimate the likelihood of annual lake volumes remaining consistent, increasing, or decreasing through the year 2067.

Of the five lakes, Sibley Lake was the most likely to sustain a long-term fishery for a period longer than 50 years. The simulated lake volumes for Alkaline Lake, Big Mallard Marsh, and Remmick Lake indicated the lakes have a 50-percent chance to fall below 75 percent of their 2016 volume by about 2030, 2067, and 2025, respectively. Simulation results for Marvin Miller Lake were substantially different compared to the other four lakes and indicated the lake has a 50-percent chance to fall below 75 percent of its 2016 volume prior to 2025.

Assessing hazards and risks at the Department of the Interior—A workshop report

Released March 11, 2019 13:33 EST

2019, Circular 1453

Nathan Wood, Alice Pennaz, Kristin Ludwig, Jeanne Jones, Kevin Henry, Jason Sherba, Peter Ng, Jason Marineau, John Juskie

On February 27–28, 2018, the U.S. Geological Survey and Department of the Interior (DOI) Office of Emergency Management (OEM) hosted a workshop to gather input from DOI subject matter experts (SMEs), resource managers, facility managers, emergency managers, and law enforcement personnel. Workshop goals were to (1) determine how DOI Bureaus and Offices use risk information for strategic planning and decision-making; (2) understand what types of information are most useful to DOI Bureaus and Offices; (3) establish what data, information, and products are desired; (4) identify the most effective methods for delivery and visualization; and (5) collect ideas for future project directions. The workshop findings presented in this report will influence the development of risk-information products created by the Strategic Hazard Identification and Risk Assessment of Department of the Interior Resources (SHIRA) Project team.

Water quality and hydrology of the Yellow Dog and Salmon Trout Watersheds, Marquette County, Michigan 2013–16

Released March 11, 2019 09:15 EST

2019, Scientific Investigations Report 2018-5152

Christopher J. Hoard, Thomas L. Weaver

In 2013, the U.S. Geological Survey, in cooperation with the Keweenaw Bay Indian Community, began monitoring the water quality of springs and seeps within the Yellow Dog and Salmon Trout watersheds in Marquette County, Michigan. The objectives of this study were to (1) monitor streamflow and analyze the hydrology of the watersheds and (2) characterize the water quality in the watersheds prior to development of mineral resources within the watershed. Three continuous-record streamgages (U.S. Geological Survey stations 04043238, 04043244, and 04043275) were examined to identify runoff and baseflow components of streamflow and the relative magnitudes of those components. Streamflow at each station was dominated by groundwater discharge with about 70 to 80 percent of the annual streamflow being groundwater-derived baseflow.

From May 2013 to October 2016, 239 water-quality samples were collected at 15 stations within the Yellow Dog and Salmon Trout watersheds. Of the 15 stations sampled, 8 of the stations were springs and 7 of the stations were streams. Samples were analyzed for nutrient, trace metal, and major-ion species at all stations with additional suspended-sediment samples collected at the 7 stream stations. Where applicable, water-quality results were compared to aquatic health guidelines used by the Michigan Department of Environmental Quality. Copper concentrations exceeded the final chronic value five times and the aquatic maximum value once, whereas silver concentrations exceeded the final chronic value twice and the aquatic maximum value once. Results indicate that chloride concentrations may be increasing at some stations, but values are generally low with a median concentration of 0.25 milligram per liter.

Bed-sediment chemistry was evaluated twice for each stream sampling station. Samples were collected in the first and last year of the study and analyzed for trace metals. Sediment chemistry results were compared to consensus-based sediment quality guidelines. None of the metal constituents analyzed exceeded the threshold effect concentration or probable effect concentration thresholds, indicating a healthy aquatic environment in relation to bed-sediment quality.

Mississippi river sediment diversions and coastal wetland sustainability: Synthesis of responses to freshwater, sediment, and nutrient inputs

Released March 09, 2019 13:53 EST

2019, Estuarine, Coastal and Shelf Science

Tracy Elsey-Quirk, Sean A. Graham, Irving A. Mendelssohn, Gregg Snedden, John W. Day, Gary P. Shaffer, Leigh Anne Sharp, Robert R. Twilley, James Pahl, R.R. Lane

Management and restoration of coastal wetlands require insight into how inundation, salinity, and the availability of mineral sediment and nutrients interact to influence ecosystem functions that control sustainability. The Mississippi River Delta, which ranks among the world's largest and most productive coastal wetland complexes, has experienced extensive deterioration over the last century due, in large part, to enhanced vulnerability to relative sea-level rise and lateral erosion caused by a combination of natural processes and anthropogenic modifications of hydrology. This land loss crisis has prompted the State of Louisiana to develop a comprehensive restoration plan that includes constructing and implementing a series of large-scale sediment diversions that will reconnect sediment- and nutrient-rich Mississippi River water to adjacent bays, estuaries, and wetlands. Sediment loading through diversions is predicted to enhance the long-term sustainability of coastal wetlands; however, the additive effects of increased inundation, abrubt changes in the salinity regime, and high nutrient loads on wetland plant growth and organic matter (SOM) decomposition rates, which help regulate accretion and elevation change, is uncertain. Therefore, this review attempts to synthesize existing information to inform predictions of the interactive effects of diversions on these drivers of coastal wetland sustainability. The data suggest that sediment deposition within an optimal elevation range will increase the overall productivity of existing wetlands where prolonged flooding does not counter this effect by limiting plant growth. A reduction in salinity may increase plant productivity and cause vegetation shifts to less salt tolerant species, but seasonal swings in salinity may have unforeseen consequences. Nutrient-loading is predicted to lead to greater aboveground productivity, which, in turn, can facilitate additional sediment trapping; however, belowground productivity may decline, particularly in areas where sediment deposition is limited. In areas experiencing net deposition, nutrient-enrichment is predicted to enhance belowground growth into new sediment and contribute to positive effects on soil organic matter accumulation, accretion, and elevation change. Thus, we contend that sediment input is essential for limiting the negative effects of flooding and nutrient-enrichment on wetland processes. These conclusions are generally supported by the biophysical feedbacks occurring in existing prograding deltas of the Mississippi River Delta complex.

Stream characteristics associated with feeding type in silver(Ichthyomyzon unicuspis) and northern brook (I. fossor) lampreys and tests for phenotypic plasticity

Released March 08, 2019 15:01 EST

2019, Environmental Biology of Fishes

Fraser Neave, Todd B. Steeves, Thomas C. Pratt, Robert L. McLaughlin, Jean V. Adams, Margaret F. Docker

In most lamprey genera, “paired” species exist in which the larvae are morphologically indistinguishable but adult feeding type differs. The lack of diagnostic genetic differences in many pairs has led to suggestions that they constitute a single gene pool with environmentally influenced feeding types. To investigate whether stream characteristics are correlated with feeding type in the parasitic silver lamprey Ichthyomyzon unicuspis and nonparasitic northern brook lamprey I. fossor, eight variables (pH, alkalinity, conductivity, discharge, total dissolved solids, and density of larval sea lamprey Petromyzon marinus, Ichthyomyzon spp., and total larval density) were compared among eight streams with only silver lamprey, 10 with only northern brook lamprey, and 13 with both species, using classification tree analysis. The most parsimonious model had a 24% misclassification rate, with silver lamprey tending to inhabit streams with higher sea lamprey larval density and northern brook lamprey tending to inhabit streams with higher Ichthyomyzon larval density. We then conducted a pilot study investigating phenotypic plasticity in a lab-based common garden experiment and an in situ transplant experiment. These studies encountered myriad difficulties and were unable to demonstrate plasticity, but did identify challenges associated with culturing Ichthyomyzon larvae. Development of effective rearing procedures for Ichthyomyzon lampreys is essential for any future similar studies.

Resource concentration mechanisms facilitate foraging success in simulations of a pulsed oligotrophic wetland

Released March 08, 2019 14:20 EST

2019, Landscape Ecology

Simeon Yurek, Donald L. DeAngelis


Movement of prey on hydrologically pulsed, spatially heterogeneous wetlands can result in transient, high prey concentrations, when changes in landscape features such as connectivity between flooded areas alternately facilitate and impede prey movement. Predators track and exploit these concentrations, depleting them as they arise.


We sought to describe how prey pulses of fish rapidly form and persist on wetland landscapes, while enduring constant consumption by wading birds, without being fully depleted. Specifically, we questioned how is the predator–prey relationship mediated by interactions between animal movement and dynamic landscape connectivity?


Two models were developed of the predator–prey-landscape system with qualitatively different representations of space, to identify and quantify prey pulsing dynamics that were robust across modeled assumptions. The first included a homogeneous landscape described by simple geometry, and implicit fish movement as wetland volume contracts. The second modeled transverse movement across a heterogeneous landscape, with isolated drying patches.


Both models produced rapid fish prey concentrations as the wetland dried to shallow water depths. These conditions are critical for making prey available to wading birds. Fish were also rapidly depleted by birds, representing daily caloric intake supporting birds. Model 1 provided average estimates across the modeled domain. Model 2 mapped locations of emerging prey hotspots on the landscape through time.


Our models tracked predator, prey, and landscape dynamics in parallel, inducing systems dynamics from empirical observations. Explicit inclusion of dynamic wetland hydrologic connectivity, a key landscape mechanism, allowed for a comprehensive picture of links between landscape dynamics and the adapted predator–prey system.

The Mw 6.0 South Napa earthquake of August 24, 2014—Observations of surface faulting and ground deformation, with recommendations for improving post-earthquake field investigations

Released March 08, 2019 10:29 EST

2019, Open-File Report 2019-1018

Daniel J. Ponti, Carla M. Rosa, James Luke Blair

The Mw 6.0 South Napa earthquake of August 24, 2014, produced complex and extensive surface faulting and other ground deformation features. Following the event, geologists made more than 1,200 field observations at locations where tectonic faulting and ground failure produced visible deformation that fractured and disturbed the ground surface. At a few locations, large-scale, detailed, field-based maps of fault rupture and ground deformation were produced. The South Napa earthquake response was one of the first times when post-earthquake reconnaissance data were mostly collected and disseminated electronically. The advantages and opportunities these new methods bring to our research also pose new challenges to large-scale compilation efforts and demonstrate the value of developing guidelines and better standardization across the community to more optimally utilize developing technology in future post-earthquake investigations. Some suggestions for standardizing the collection and dissemination of post-earthquake field reconnaissance data are provided herein.

Field observations and maps were integrated with airborne imagery, lidar, and InSAR to produce a comprehensive, large-scale digital map of fault rupture and zones of ground deformation. The map, observations, and photo database are summarized here in appendixes and figures and are also available as a series of digital data products within a companion U.S. Geological Survey data release (Ponti and others, 2019); the characteristics of fault rupture and ground deformation features are summarized in detail in the body of this report.

The results of this compilation reveal that faulting occurred within a 2-km-wide zone on six, roughly parallel traces within the West Napa Fault System. Most of the fault slip, and all the afterslip, occurred on the 21-km-long westernmost trace (Trace A). Maximum coseismic slip was greater than 40 cm and possibly as great as 60 cm, with the slip maximum located about 10 km north of the epicenter. Extensive ground deformation also occurred off the principal fault traces. Deformation characteristics of these features were not consistent with either primary faulting or shaking-induced ground failure and remain enigmatic, although this report includes speculation about possible origins.

The use of InSAR was invaluable for identifying and mapping secondary traces with small displacements, and for delineating the overall details of the extensive rupture. InSAR data also highlighted other areas with possible ground deformation—some of which are found coincident with previously mapped fault traces, whereas others are in areas where no faults were previously mapped. Several of these regions had no visible ground deformation, whereas others did produce features that were inconsistent with tectonic faulting, so care must be taken not to over interpret the InSAR data without careful, corroborating field investigations.

Flooding regimes increase avian predation on wildlife prey in tidal marsh ecosystems

Released March 08, 2019 10:14 EST

2019, Ecology and Evolution (9) 1083-1094

Karen M. Thorne, Kyle A. Spragens, Kevin J. Buffington, Jordan A. Rosencranz, John Takekawa

Within isolated and fragmented populations, species interactions such as predation can cause shifts in community structure and demographics in tidal marsh ecosystems. It is critical to incorporate species interactions into our understanding when evaluating the effects of sea‐level rise and storm surges on tidal marshes. In this study, we hypothesize that avian predators will increase their presence and hunting activities during high tides when increased inundation makes their prey more vulnerable. We present evidence that there is a relationship between tidal inundation depth and time of day on the presence, abundance, and behavior of avian predators. We introduce predation pressure as a combined probability of predator presence related to water level. Focal surveys were conducted at four tidal marshes in the San Francisco Bay, California where tidal inundation patterns were monitored across 6 months of the winter. Sixteen avian predator species were observed. During high tide at Tolay Slough marsh, ardeids had a 29‐fold increase in capture attempts and 4 times greater apparent success rate compared with low tide. Significantly fewer raptors and ardeids were found on low tides than on high tides across all sites. There were more raptors in December and January and more ardeids in January than in other months. Ardeids were more prevalent in the morning, while raptors did not exhibit a significant response to time of day. Modeling results showed that raptors had a unimodal response to water level with a peak at 0.5 m over the marsh platform, while ardeids had an increasing response with water level. We found that predation pressure is related to flooding of the marsh surface, and short‐term increases in sea levels from high astronomical tides, sea‐level rise, and storm surges increase vulnerability of tidal marsh wildlife.

An introduced breeding population of Chrysemys picta marginata in the Kaibab National Forest, northern Arizona

Released March 08, 2019 10:12 EST

2019, Current Herpetology (38) 91-98

Jeffrey E. Lovich, Bruce L. Christman, Jenna Norris, Kristy L. Cummings, Shellie R. Puffer, Christina Jones

The painted turtle (Chrysemys picta) is widely distributed from coast to coast in North America with each of four subspecies generally occupying different regions. In the southwestern USA and northern Mexico, where C. p. bellii is the expected native race, populations are small and widelyscattered. Introduced populations of other painted turtle subspecies are reported from various locations in the USA. We discovered a small but dense introduced population of C. p. marginata on the Colorado Plateau in northern Arizona, a region with few, if any, turtles due to aridity and an elevated topography with little surface water. The turtles were in a remote pond constructed to provide cattle with water. Chrysemys p. marginata occur naturally east of the Mississippi River, over 2,000 km away. The nearest native population of C. p. bellii in Arizona is over 160 km away. We observed nesting females, juveniles, and the presence of shelled eggs in females via Xradiography confirming a self-sustaining population. The body sizes and nesting season we observed were consistent with data for those variables from native populations of the taxon. It is unknown exactly how the turtles came to be established in such a remote location, but it is unlikely that they will spread due to the scarcity of perennial water sources in the semi-arid region. Due to increasing drought frequency and duration in the region, small populations like this one, introduced into a novel environment, may be bellwethers for monitoring the effects of climate change.

Seismic hazard assessment at the Fallon, Nevada, Frontier Observatory for Research in Geothermal Energy site

Released March 08, 2019 09:23 EST

2019, Open-File Report 2019-1020

J. Ole Kaven, Ernest L. Majer, William Foxall, Eric L. Sonnenthal, William Pettitt

Enhanced geothermal systems (EGS) technology aims to engineer a productive geothermal reservoir in regions of hot, but low permeability, rocks. In any EGS operation, the rock mass requires stimulation by high pressure injection of fluids, which has the potential to induce seismicity. To address the seismic hazard specifically, a probabilistic seismic hazard assessment (PSHA) is often required and is generally part of an induced seismicity mitigation plan (ISMP). A specific PSHA for the proposed Fallon, Nev., FORGE site is outlined below that relies solely on hypothetical stimulation scenarios and analog sites to assess the hazard of induced seismicity in the absence of local microseismicity. Partially due to the lack of existing seismicity at the site and partially to arrive at conservative estimates of the hazard, the PSHA is calculated for a range of b-values. Results indicate that the conservative estimates of seismic hazard at locations having significant, sensitive infrastructure near the proposed site are very low.

Invasive plant species

Released March 07, 2019 16:40 EST

2019, Book chapter, Encyclopedia of ecology

Beth A. Middleton

Invasive species may be one of the worts environmental problems facing the conservation of natural areas, because of their role in changing ecosystem function. At the same time, invasive species cause much human suffering and economic loss. The approach to eliminating invasive species can be improved by a better understanding of the various types of invasive species, and the scientific hypotheses surrounding their ability to invade novel environments. Despite the billions of dollars spent each year, invasive species are difficult if not impossible to eliminate after they have established. Various methods of eliminating plant species from natural communities are described in this review. An increased understanding of the nature of invasive species including their genetic relationship to their progenitors, hypotheses regarding their invasive qualities, and effective approaches for their removal from ecosystems are all sorely needed. Volunteers can help in the invasive species effort by working on local plant/animal removal projects, reporting invasive species sightings to appropriate officials, or working with scientists to collect basic data for ecological research.

Mercury speciation and retention in a salt marsh undergoing long-term fertilization

Released March 07, 2019 16:35 EST

2019, Estuarine, Coastal and Shelf Science (218) 188-196

Carl Lamborg, Tracy Mincer, William Buchanan, Caroline Collins, Gretchen Swarr, Priya M. Ganguli, Kristen Whalen, Michael H. Bothner, Ivan Valiela

Experimental plots in Great Sippewissett Marsh (Falmouth, MA USA) have been undergoing long-term (>48 years) fertilization through the application of commercial sewage sludge-based fertilizer. The experimental treatment focuses on the effect of added nitrogen on the salt marsh plots, but also supplies mercury (Hg) and other metals. This experiment provides a unique opportunity to test hypotheses regarding the Hg-related response of coastal marine ecosystems to eutrophication as well as assess the efficacy of salt marshes as sinks for increased loadings of Hg to the coastal zone. Hg inventories in sediments of control plots were similar to loadings from atmospheric deposition and inventories in the fertilized plots closely reflected the estimated loadings of Hg contained in the added fertilizer. In both the control and fertilized plots, distribution of Hg appeared somewhat different than the history of loadings, implying some level of Hg mobility. The relative abundance of monomethylmercury (CH3Hg+) within the plots varied with the amount of fertilizer applied with the highest percentage of Hg as CH3Hg+ found in the control plots, and the lowest percentages of CH3Hg+ and S were measured in plots fertilized at the highest dose. The results from this marsh suggest that eutrophication indirectly lowers CH3Hg+ production in this particular ecosystem, but perhaps not as a result of the sequestration of Hg(II) with S.

Flood-inundation maps for Lake Champlain in Vermont and New York

Released March 07, 2019 16:15 EST

2019, Scientific Investigations Report 2018-5169

Robert H. Flynn, Laura Hayes

In 2016, digital flood-inundation maps along the shoreline of Lake Champlain in Addison, Chittenden, Franklin, and Grand Isle Counties in Vermont and northern Clinton County in New York were created by the U.S. Geological Survey (USGS) in cooperation with the International Joint Commission (IJC). This report discusses the creation of updated static digital flood-inundation mapping, in 2018, to include the entire shoreline of Lake Champlain in the United States. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science website at http://water.usgs.gov/osw/flood_inundation/, depict estimates of the areal extent of flooding corresponding to selected water-surface elevations (stages) at the USGS lake gages on Lake Champlain.

As a result of the record setting floods of May 2011 in Lake Champlain and the Richelieu River, the U.S. and Canadian governments requested that the IJC issue a reference for a study to identify how flood forecasting, preparedness, and mitigation could be improved in the Lake Champlain–Richelieu River Basin. The IJC submitted the Lake Champlain–Richelieu River Plan of Study to the governments of Canada and the United States in 2013. The flood-inundation maps in this study are one aspect of the task work outlined in the IJC 2013 Plan of Study.

Wind and seiche effects (standing oscillating wave with a long wavelength) that can influence flooding along the Lake Champlain shoreline were not represented. The flood-inundation maps reflect 11 stages for Lake Champlain that are static for the entire area of the lake. Near-real-time stages at the USGS gages on Lake Champlain may be obtained from the USGS National Water Information System website at http://waterdata.usgs.gov/ (https://doi.org/10.5066/F7P55KJN) or from the National Weather Service Advanced Hydrologic Prediction Service at http://water.weather.gov/ahps/.

Updated static flood-inundation boundary extents were created for Lake Champlain in Franklin, Chittenden, Addison, Rutland, and Grand Isle Counties in Vermont and Clinton, Essex, and Washington Counties in New York by using recently acquired (2009, 2012, 2014, and 2015) light detection and ranging (lidar) data. The corresponding flood-inundation maps may be referenced to any of the four active USGS lake gages on Lake Champlain. Of these four active lake gages, USGS lake gage 04295000, Richelieu River (Lake Champlain) at Rouses Point, N.Y.; USGS lake gage 04294500, Lake Champlain at Burlington, Vt.; USGS lake gage 04279085 Lake Champlain north of Whitehall, N.Y.; and USGS lake gage 04294413, Lake Champlain at Port Henry, N.Y., only the Richelieu River (Lake Champlain) at Rouses Point, N.Y., gage also serves as a National Weather Service prediction location. Lake Champlain static flood-inundation map boundary extents corresponding to the May 2011 peak flood stage (103.20 feet [ft], National Geodetic Vertical Datum of 1929 [NGVD 29], as recorded at the USGS Rouses Point lake gage, were compared to the flood-inundation area extents determined from satellite imagery for the May 2011 flood (which incorporated documented high-water marks from the flood of May 2011) and were found to be in good agreement. The May 2011 flood is the highest recorded lake water level (stage) at the Rouses Point, N.Y., and Burlington, Vt., lake gages. Flood stages greater than 101.5 ft (NGVD 29) exceed the “major flood stage” as defined by the National Weather Service for USGS lake gage 04295000.

Updated digital elevation models (DEMs) were created from the recent lidar data for Lake Champlain in Vermont and New York. These DEMs were used in determining the flood-inundation boundary and associated depth grids for 11 flood stages at 0.5-ft or 1-ft intervals from 100.0 to 106.0 ft (NGVD 29) as referenced to the USGS lake gages. In addition, the May 2011 flood-inundation area for elevation 103.20 ft (NGVD 29) (102.77 ft, North American Vertical Datum of 1988) was determined from these updated DEMs.

The availability of these maps, along with online information regarding current stages at the USGS lake gages and forecasted high-flow stages from the National Weather Service at USGS lake gage 04295000, Richelieu River (Lake Champlain) at Rouses Point, N.Y., 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 post-flood recovery efforts.

Florida Coastal Mapping Program—Overview and 2018 workshop report

Released March 07, 2019 15:45 EST

2019, Open-File Report 2019-1017

Cheryl J. Hapke, Philip A. Kramer, Elizabeth H. Fetherston-Resch, Rene D. Baumstark, Ryan Druyor, Xan Fredericks, Ekaterina Fitos

The Florida Coastal Mapping Program is a nascent but highly relevant program that has the potential to greatly enhance the “Blue Economy” of Florida by coordinating and facilitating sea-floor mapping efforts and aligning partner and stakeholder activities for increased efficiency and cost reduction. Sustained acquisition of modern coastal mapping information for Florida may improve management of resources and reduce costs by eliminating redundancy. Economic growth could be aided by improved data to support emerging sectors such as aquaculture and renewable energy.

The present focus of the Florida Coastal Mapping Program is on modern, high-resolution bathymetric and coastal topobathymetric data, which can be immediately used to update navigational charts and identify navigation hazards, provide fundamental baseline data for scientific research, and provide information for use by emergency managers and responders. Derivative products include identifying sand resources for beach nourishment, creating vastly improved models for coastal erosion and flooding, identifying coastal springs, and creating benthic habitat maps. The uses and applications of the data generated could grow over time. The process of creating a steering committee and technical team, conducting an inventory and gaps analysis, soliciting feedback from the stakeholder and partner communities, and developing a prioritization process has provided a framework on which a successful program can develop a sustainable funding strategy that may be an investment the citizens of Florida could benefit from for decades.

Validating a time series of annual grass percent cover in the sagebrush ecosystem

Released March 07, 2019 13:05 EST

2019, Rangeland Ecology and Management (72) 347-359

Stephen P. Boyte, Bruce K. Wylie, Donald J. Major

We mapped yearly (2000–2016) estimates of annual grass percent cover for much of the sagebrush ecosystem of the western United States using remotely sensed, climate, and geophysical data in regression-tree models. Annual grasses senesce and cure by early summer and then become beds of fine fuel that easily ignite and spread fire through rangeland systems. Our annual maps estimate the extent of these fuels and can serve as a tool to assist land managers and scientists in understanding the ecosystem’s response to weather variations, disturbances, and management. Validating the time series of annual maps is important for determining the usefulness of the data. To validate these maps, we compare Bureau of Land Management Assessment Inventory and Monitoring (AIM) data to mapped estimates and use a leave-one-out spatial assessment technique that is effective for validating maps that cover broad geographical extents. We hypothesize that the time series of annual maps exhibits high spatiotemporal variability because precipitation is highly variable in arid and semiarid environments where sagebrush is native, and invasive annual grasses respond to precipitation. The remotely sensed data that help drive our regression-tree model effectively measures annual grasses’ response to precipitation. The mean absolute error (MAE) rate varied depending on the validation data and technique used for comparison. The AIM plot data and our maps had substantial spatial incongruence, but despite this, the MAE rate for the assessment equaled 12.62%. The leave-one-out accuracy assessment had an MAE of 8.43%. We quantified bias, and bias was more substantial at higher percent cover. These annual maps can help management identify actions that may alleviate the current cycle of invasive grasses because it enables the assessment of the variability of annual grass  percent cover distribution through space and time, as part of dynamic systems rather than static systems.

Evidence for plunging river plume deposits in the Pahrump Hills member of the Murray formation, Gale crater, Mars

Released March 07, 2019 11:15 EST

2019, Sedimentology

Kathryn M. Stack, John P. Grotzinger, Michael P. Lamb, Sanjeev Gupta, David M. Rubin, Linda C. Kah, Lauren A. Edgar, Deirdra M. Fey, Joel A. Hurowitz, Marie J. McBride, Frances Rivera-Hernández, Dawn Y. Sumner, Jason K. Van Beek, Rebecca M. E. Williams, R. Aileen Yingst

Recent robotic missions to Mars have offered new insights into the extent, diversity and habitability of the Martian sedimentary rock record. Since the Curiosity rover landed in Gale crater in August 2012, the Mars Science Laboratory Science Team has explored the origins and habitability of ancient fluvial, deltaic, lacustrine and aeolian deposits preserved within the crater. This study describes the sedimentology of a ca 13 m thick succession named the Pahrump Hills member of the Murray formation, the first thick fine‐grained deposit discovered in situ on Mars. This work evaluates the depositional processes responsible for its formation and reconstructs its palaeoenvironmental setting. The Pahrump Hills succession can be sub‐divided into four distinct sedimentary facies: (i) thinly laminated mudstone; (ii) low‐angle cross‐stratified mudstone; (iii) cross‐stratified sandstone; and (iv) thickly laminated mudstone–sandstone. The very fine grain size of the mudstone facies and abundant millimetre‐scale and sub‐millimetre‐scale laminations exhibiting quasi‐uniform thickness throughout the Pahrump Hills succession are most consistent with lacustrine deposition. Low‐angle geometric discordances in the mudstone facies are interpreted as ‘scour and drape’ structures and suggest the action of currents, such as those associated with hyperpycnal river‐generated plumes plunging into a lake. Observation of an overall upward coarsening in grain size and thickening of laminae throughout the Pahrump Hills succession is consistent with deposition from basinward progradation of a fluvial‐deltaic system derived from the northern crater rim into the Gale crater lake. Palaeohydraulic modelling constrains the salinity of the ancient lake in Gale crater: assuming river sediment concentrations typical of floods on Earth, plunging river plumes and sedimentary structures like those observed at Pahrump Hills would have required lake densities near freshwater to form. The depositional model for the Pahrump Hills member presented here implies the presence of an ancient sustained, habitable freshwater lake in Gale crater for at least ca 103 to 107 Earth years.

Structure contour and overburden maps of the Niobrara interval of the Upper Cretaceous Cody Shale in the Wind River Basin, Wyoming

Released March 07, 2019 11:15 EST

2019, Scientific Investigations Map 3427

Thomas M. Finn

The Wind River Basin in central Wyoming is one of many structural and sedimentary basins that formed in the Rocky Mountain foreland during the Laramide orogeny. The basin is bounded by the Washakie, Owl Creek, and southern Bighorn uplifts on the north, the Casper arch on the east, the Granite Mountains uplift on the south, and Wind River uplift on the west.

The first commercial oil well in Wyoming was drilled at Dallas dome near an oil seep along the southwestern edge of the Wind River Basin in 1884. Since then, many important conventional oil and gas fields, that produce from reservoirs ranging in age from Mississippian through Tertiary, have been discovered in this basin. In addition, an extensive unconventional (continuous) overpressured basin-centered gas accumulation has been identified in Cretaceous and Tertiary strata in the deeper parts of the basin. It has been suggested that various Upper Cretaceous marine shales, including the Cody Shale, are the principal hydrocarbon source rocks for many of these accumulations. With recent advances in horizontal drilling and multistage fracture stimulation, there has been an increase in exploration and completion of wells in equivalent marine shales in other Rocky Mountain Laramide basins that were traditionally thought of only as hydrocarbon source rocks. The maps presented in this report were constructed as part of a project carried out by the U.S. Geological Survey to characterize the geologic framework of potential undiscovered continuous (unconventional) oil and gas resources of the Niobrara interval of the Upper Cretaceous Cody Shale in the Wind River Basin in central Wyoming.

Coastal habitat change and marine megafauna behavior: Florida manatees encountering reduced food provisions in a prominent winter refuge

Released March 07, 2019 10:09 EST

2019, Endangered Species Research (38) 29-43

Chanda J. Littles, Robert K. Bonde, Susan M. Butler, Charles A. Jacoby, Sky K. Notestein, James P. Reid, Daniel H. Slone, Thomas K. Frazer

A decline in submerged aquatic vegetation (SAV) within Florida’s spring-fed thermal refuges raises questions about how these systems support winter foraging of Florida manatees Trichechus manatus latirostris. We analyzed telemetry data for 12 manatees over 7 yr to assess their use of Kings Bay, a winter refuge with diminished SAV. After accounting for the effect of water temperature, we hypothesized that the number of trips out of Kings Bay would increase and the time wintering manatees spent in Kings Bay would decrease. Trips out of and into Kings Bay were also compared to assess potential influences on exiting or entering. There were no detectable differences in the number of trips out of the bay or overall time manatees spent in Kings Bay across winters. The percentage of time water temperatures were below 20°C was the single best predictor of increased time spent in Kings Bay. Trips out of Kings Bay were more likely than trips into the bay to occur after 12:00 h and during a high but ebbing tide. Nine manatees tracked for longer than 75 d in winter spent 7 to 57% of their time in the Gulf of Mexico, and 3 of these manatees spent 7 to 65% of the winter >80 km from the mouth of Kings Bay. Results suggest the low amount of SAV in Kings Bay does not obviate its use by manatees, though there are likely tradeoffs for manatees regularly foraging elsewhere. Accounting for movements of Florida manatees through a network of habitats may improve management strategies and facilitate desirable conservation outcomes.

The past and future roles of competition and habitat in the range‐wide occupancy dynamics of Northern Spotted Owls

Released March 07, 2019 10:05 EST

2019, Ecological Applications

Charles B. Yackulic, Larissa L. Bailey, Catherine Dugger, Raymond J. Davis, Alan B. Franklin, Eric D. Forsman, Steven H. Ackers, Lawrence S. Andrews, Lowell V. Diller, Scott A. Gremel, Keith A. Hamm, Dale R. Herter, J. Mark Higley, Rob B. Horn, Christopher McCafferty, Janice A. Reid, Jeremy T. Rockweit, Stan G. Sovern

Slow ecological processes challenge conservation. Short‐term variability can obscure the importance of slower processes that may ultimately determine the state of a system. Furthermore, management actions with slow responses can be hard to justify. One response to slow processes is to explicitly concentrate analysis on state dynamics. Here, we focus on identifying drivers of Northern Spotted Owl (Strix occidentalis caurina) territorial occupancy dynamics across 11 study areas spanning their geographic range and forecasting response to potential management actions. Competition with Barred Owls (Strix varia) has increased Spotted Owl territory extinction probabilities across all study areas and driven recent declines in Spotted Owl populations. Without management intervention, the Northern Spotted Owl subspecies will be extirpated from parts of its current range within decades. In the short term, Barred Owl removal can be effective. Over longer time spans, however, maintaining or improving habitat conditions can help promote the persistence of northern spotted owl populations. In most study areas, habitat effects on expected Northern Spotted Owl territorial occupancy are actually greater than the effects of competition from Barred Owls. This study suggests how intensive management actions (removal of a competitor) with rapid results can complement a slower management action (i.e., promoting forest succession).

Spatial distribution of nutrients, chloride, and suspended sediment concentrations and loads determined by using different sampling methods in a cross section of the Trenton Channel of the Detroit River, Michigan, November 2014–November 2015

Released March 07, 2019 10:00 EST

2019, Scientific Investigations Report 2018-5141

Alexander R. Totten, Joseph W. Duris

The Detroit River separates the United States and Canada as it flows from Lake St. Clair to Lake Erie. The Trenton Channel is a 13-kilometer-long branch of the Detroit River that flows to the west of Grosse Ile before rejoining the Detroit River near its mouth, just before the Detroit River flows into Lake Erie. The U.S. Environmental Protection Agency has listed both the Trenton Channel and Detroit River as Areas of Concern because of a list of Beneficial Use Impairments such as interrupted drinking-water services, loss of aquatic life, and reduced recreational use. Phosphorus loading from tributaries such as the Trenton Channel is one of the primary drivers of eutrophication in Lake Erie. The complex flow patterns and variable distribution of chemical constituents in the Trenton Channel make it difficult to accurately characterize the concentrations and loads of nutrients and other constituents conveyed through the channel to Lake Erie.

In order to better understand the Trenton Channel’s contributions of nutrients (total phosphorus, orthophosphate, total nitrogen, and ammonia), chloride, and suspended sediment to Lake Erie and evaluate differences in results obtained by using different sample methodologies, the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency and Environment Canada, completed 12 sampling campaigns on the Trenton Channel in Detroit, Michigan, from November 2014 through November 2015.

Acoustic Doppler current profiler (ADCP) techniques were used to characterize the distribution of velocity components within a cross section corresponding to a transect of the Trenton Channel at U.S. Geological Survey station 041686401 Trenton Channel of Detroit River at Grosse Ile, Mich. Three methods of collecting water-quality data at the same transect of the Trenton Channel were used: multiple-vertical depth-integrated (MVDI), fixed-point, and discrete samples. Horizontal and vertical variations in concentrations of nutrients, chloride, and suspended sediment were analyzed from discrete samples to better understand distributions of these constituents throughout the channel. Constituent loads were calculated by using individual sample concentrations and ADCP measurements for discharge made on the same day that the water-quality samples were collected. Constituent loads calculated from MVDI and fixed-point sampling methods were compared. The relation between MVDI and fixed-point samples helped quantify the differences between the sampling methods. Linear regression equations depicting the relation between concentrations measured by using MVDI and fixed-point samples were prepared.

ADCP data indicates that velocities throughout the sampled transect remain uniform except for one location around 200 meters from the west bank of the channel. Secondary flow vectors suggest the presence of counter-rotating helical flow cells, and these helical flow cells could affect the mixing of constituents in transport by preventing cross-channel mixing. Flow discharges throughout the sampling campaign showed small variations, although lower flow rates were observed in the early winter months than in the summer months. Discrete sampling methods results displayed both heterogeneity throughout the channel horizontally, representing limited horizontal mixing in the channel, and displayed homogeneity throughout vertical transects, indicating mixing vertically. Comparisons between MVDI and fixed-point methods found consistently higher concentrations were measured in MVDI samples compared to concentrations measured in fixed-point samples. To correct for this bias between MVDI and fixed-point sample results, simple linear-regression equations were developed for all major constituents to help estimate constituent concentrations from fixed-point samples equivalent to those measured by using MVDI sampling techniques. Instantaneous constituent loads were developed by using velocity and discharge data obtained from ADCPs and constituent concentrations obtained from MVDI and fixed-point samples.

Where has turtle ecology been, and where is it going?

Released March 07, 2019 09:40 EST

2019, Herpetologica (75) 4-20

J. Whitfield Gibbons, Jeffrey E. Lovich

Over 9000 articles have been published on turtles and tortoises (excluding sea turtles) since 1950 according to the Web of Science, including over 8000 contained in a personal bibliography that we analyze in this paper. Research had a slow start from 1900 to 1950, with mostly anecdotal additions to our knowledge until the contributions of F. Cagle and A. Carr took turtle research to new levels as the cofathers of turtle ecology in the middle of the last century. Books written in 1939, 1952, and 1972 that compiled existing literature on turtles in the United States and Canada set the stage for growing interest in turtles. The first global compilation of turtle species did not become available until 1961. Publication frequency increased in the 1960s and especially the 1970s as interest in turtles grew, and a wave of turtle biologists emerged from doctoral degree programs. We briefly review the contributions of scientists who published extensively on turtle ecology in those and later decades up to the present. We also review advances in our knowledge of various topics, including the global distribution of turtle research efforts; changes in our perceptions of turtle species diversity over time; turtle community ecology; sex ratios, sex-determination, and climate change; overwintering behavior; sexual size dimorphism and sexual dichromatism; analyses of population genetics; turtles and vocalization; and the emergence of turtle conservation biology efforts. We conclude with a discussion of future opportunities and challenges for working with turtles.

Modelling sea lice control by lumpfish on Atlantic salmon farms: interactions with mate limitation, temperature, and treatment rules

Released March 06, 2019 11:26 EST

2019, Diseases of Aquatic Organisms

Gregor F. McEwan, Maya L. Groner, Allegra A. B. Cohen, Albert K. D. Imsland, Crawford W. Revie

Atlantic salmon farming is one of the largest aquaculture sectors in the world. A major impact on farm economics, fish welfare, and potentially nearby wild salmonid populations, is the sea louse ectoparasite Lepeophtheirus salmonis. Sea louse infestations are most often controlled through application of chemicals, but in most farming regions sea lice have evolved resistance to the small set of available chemicals. Therefore, alternative treatment methodologies are becoming more widely used. One increasingly common alternative treatment involves the co-culture of farmed salmon with cleaner fish, which prey on sea lice. However, despite their wide use, little is understood about the situations in which cleaner fish are most effective. For example, previous work suggests that a low parasite density results in sea lice finding it difficult to acquire mates, reducing fecundity and population growth. Other work suggests that environmental conditions such as temperature and external sea louse pressure have substantial impact on this mate limitation threshold and may even remove the effect entirely. We use an Agent-Based Model (ABM) to simulate cleaner fish on a salmon farm to explore interactions between sea louse mating behaviour, cleaner fish feeding rate, temperature, and external sea lice pressure. We found that sea louse mating has a substantial effect on sea louse infestations under a variety of environmental conditions. Our results suggest that cleaner fish can control sea louse infestations most effectively by maintaining the population below critical density thresholds.

Not so normal normals: Species distribution model results are sensitive to choice of climate normals and model type

Released March 06, 2019 11:22 EST

2019, Climate (7) 1-15

Catherine S. Jarnevich, Nicholas E. Young

Species distribution models have many applications in conservation and ecology, and climate data are frequently a key driver of these models. Often, correlative modeling approaches are developed with readily available climate data; however, the impacts of the choice of climate normals is rarely considered. Here, we produced species distribution models for five disparate species using four different modeling algorithms and compared results between two different, but overlapping, climate normals time periods. Although the correlation structure among climate predictors did not change between the time periods, model results were sensitive to both baseline climate period and model method, even with model parameters specifically tuned to a species. Each species and each model type had at least one difference in variable retention or relative ranking with the change in climate time period. Pairwise comparisons of spatial predictions were also different, ranging from a low of 1.6% for climate period differences to a high of 25% for algorithm differences. While uncertainty from model algorithm selection is recognized as an important source of uncertainty, the impact of climate period is not commonly assessed. These uncertainties may affect conservation decisions, especially when projecting to future climates, and should be evaluated during model development.

Patterns of mercury and selenium exposure in Minnesota common loons

Released March 06, 2019 11:18 EST

2019, Environmental Toxicology and Chemistry (38) 524-532

Kevin P. Kenow, Steven C. Houdek, Luke J. Fara, Richard A. Erickson, Brian R. Gray, Travis J. Harrison, Bruce Monson, Carrol L. Henderson

Common loons (Gavia immer) are at risk of elevated dietary mercury (Hg) exposure in portions of their breeding range. To assess the level of risk among loons in Minnesota (USA), we investigated loon blood Hg concentrations in breeding lakes across Minnesota. Loon blood Hg concentrations were regressed on predicted Hg concentrations in standardized 12‐cm whole‐organism yellow perch (Perca flavescens), based on fish Hg records from Minnesota lakes, using the US Geological Survey National Descriptive Model for Mercury in Fish. A linear model, incorporating common loon sex, age, body mass, and log‐transformed standardized perch Hg concentration representative of each study lake, was associated with 83% of the variability in observed common loon blood Hg concentrations. Loon blood Hg concentration was positively related to standardized perch Hg concentrations; juvenile loons had lower blood Hg concentrations than adult females, and blood Hg concentrations of juveniles increased with body mass. Blood Hg concentrations of all adult common loons and associated standardized prey Hg for all loon capture lakes included in the study were well below proposed thresholds for adverse effects on loon behavior, physiology, survival, and reproductive success. The fish Hg modeling approach provided insights into spatial patterns of dietary Hg exposure risk to common loons across Minnesota. We also determined that loon blood selenium (Se) concentrations were positively correlated with Hg concentration. Average common loon blood Se concentrations exceeded the published provisional threshold.

The area under the precision‐recall curve as a performance metric for rare binary events

Released March 06, 2019 11:16 EST

2019, Methods in Ecology and Evolution

Helen R. Sofaer, Jennifer A. Hoeting, Catherine S. Jarnevich

  1. Species distribution models are used to study biogeographic patterns and guide decision‐making. The variable quality of these models makes it critical to assess whether a model's outputs are suitable for the intended use, but commonly used evaluation approaches are inappropriate for many ecological contexts. In particular, unrealistically high performance assessments have been associated with models for rare species and predictions over large geographic extents.
  2. We evaluated the area under the precision‐recall curve (AUC‐PR) as a performance metric for rare binary events, focusing on the assessment of species distribution models. Precision is the probability that a species is present given a predicted presence, while recall (more commonly called sensitivity) is the probability the model predicts presence in locations where the species has been observed. We simulated species at three levels of prevalence, compared AUC‐PR and the area under the receiver operating characteristic curve (AUC‐ROC) when the geographic extent of predictions was increased and assessed how well each metric reflected a model's utility to guide surveys for new populations.
  3. AUC‐PR was robust to species rarity and, unlike AUC‐ROC, not affected by an increasing geographic extent. The major advantages of AUC‐PR arise because it does not incorporate correctly predicted absences and is therefore less prone to exaggerate model performance for unbalanced datasets. AUC‐PR and precision were useful indicators of a model's utility for guiding surveys.
  4. We show that AUC‐PR has important advantages for evaluating models of rare species, and its benefits in the context of unbalanced binary responses will make it applicable for other ecological studies. By not considering the true negative quadrant of the confusion matrix, AUC‐PR ameliorates issues that arise when the geographic extent is increased beyond the species’ range or when a large number of background points are used when absence information is unavailable. However, no single metric captures all aspects of performance nor provides an absolute index that can be compared across datasets. Our results indicate AUC‐PR and precision can provide useful and intuitive metrics for evaluating a model's utility for guiding sampling, and can complement other metrics to help delineate a model's appropriate use.

Distant neighbors: recent wildfire patterns of the Madrean Sky Islands of southwestern United States and northwestern Mexico

Released March 06, 2019 11:11 EST

2019, Fire Ecology (15) 1-20

Miguel L. Villarreal, Sandra L. Haire, Jose M. Iniguez, Citlali Cortés Montaño, Travis B. Poitras


Information about contemporary fire regimes across the Sky Island mountain ranges of the Madrean Archipelago Ecoregion in the southwestern United States and northern Mexico can provide insight into how historical fire management and land use have influenced fire regimes, and can be used to guide fuels management, ecological restoration, and habitat conservation. To contribute to a better understanding of spatial and temporal patterns of fires in the region relative to environmental and anthropogenic influences, we augmented existing fire perimeter data for the US by mapping wildfires that occurred in the Mexican Sky Islands from 1985 to 2011.


A total of 254 fires were identified across the region: 99 fires in Mexico (μ = 3901 ha, σ = 5066 ha) and 155 in the US (μ = 3808 ha, σ = 8368 ha). The Animas, Chiricahua, Huachuca-Patagonia, and Santa Catalina mountains in the US, and El Pinito in Mexico had the highest proportion of total area burned (>50%) relative to Sky Island size. Sky Islands adjacent to the border had the greatest number of fires, and many of these fires were large with complex shapes. Wildfire occurred more often in remote biomes, characterized by evergreen woodlands and conifer forests with cooler, wetter conditions. The five largest fires (>25 000 ha) all occurred during twenty-first century droughts (2002 to 2003 and 2011); four of these were in the US and one in Mexico. Overall, high variation in fire shape and size were observed in both wetter and drier years, contributing to landscape heterogeneity across the region.


Future research on regional fire patterns, including fire severity, will enhance opportunities for collaborative efforts between countries, improve knowledge about ecological patterns and processes in the borderlands, and support long-term planning and restoration efforts.

Historical background and current developments for mapping burned area from satellite Earth observation

Released March 06, 2019 11:06 EST

2019, Remote Sensing of Environment (225) 45-64

Emilio Chuvieco, Flourent Mouillot, Guido R. van der Werf, Jesús San Miguel, Mihai Tanasse, Nikos Koutsias, Mariano García, Marta Yebra, Marc Padilla, Angelika Heil, Todd J. Hawbaker, Louis Giglio

Fire has a diverse range of impacts on Earth's physical and social systems. Accurate and up to date information on areas affected by fire is critical to better understand drivers of fire activity, as well as its relevance for biogeochemical cycles, climate, air quality, and to aid fire management. Mapping burned areas was traditionally done from field sketches. With the launch of the first Earth observation satellites, remote sensing quickly became a more practical alternative to detect burned areas, as they provide timely regional and global coverage of fire occurrence. This review paper explores the physical basis to detect burned area from satellite observations, describes the historical trends of using satellite sensors to monitor burned areas, summarizes the most recent approaches to map burned areas and evaluates the existing burned area products (both at global and regional scales). Finally, it identifies potential future opportunities to further improve burned area detection from Earth observation satellites.

Spatial and temporal variability of harmful algal blooms in Milford Lake, Kansas, May through November 2016

Released March 06, 2019 07:46 EST

2019, Scientific Investigations Report 2018-5166

Guy M. Foster, Jennifer L. Graham, Lindsey R. King

The U.S. Geological Survey, in cooperation with the Kansas Department of Health and Environment (KDHE), completed a study to quantify the spatial and temporal variability of cyanobacterial blooms in Milford Lake, Kansas, over a range of environmental conditions at various time scales (hours to months). A better understanding of the spatial and temporal variability of cyanobacteria and microcystin will inform sampling and management strategies for Milford Lake and for other lakes with cyanobacterial harmful algal bloom (CyanoHAB) issues throughout the Nation. Spatial and temporal variability were assessed in the upstream one-third of Milford Lake (designated as “Zone C” by KDHE) during May through November 2016 using a combination of time-lapse photography, continuous water-quality monitors, discrete phytoplankton, chlorophyll, and microcystin samples, and spatially dense near-surface data. Combined, these data were used to characterize variability of cyanobacterial abundance, algal biomass, and microcystin concentrations in Zone C of Milford Lake before, during, and after cyanobacterial blooms in 2016.

Temporal patterns were evaluated during May through November 2016 using time-lapse photography at six locations in Zone C and at a single point location (the Wakefield site) using a combination of discrete and continuously measured water-quality data (including the cyanobacterial pigment phycocyanin). Based on time-lapse photography, CyanoHABs developed in Zone C of Milford Lake in early July and persisted through the end of November. Bloom accumulations at individual sites were dependent on wind direction. After a change in wind direction, it would take about 1 day for accumulations to become visible at different locations. During periods with low wind, accumulations were widespread and visible at all sites. Cyanobacteria were absent from the algal community at the Wakefield site in late May and were a minor component of the community in June; however, by mid-July the cyanobacteria were dominant and remained dominant until early November.

Chlorophyll and microcystin concentrations at the Wakefield site were estimated using sensor-measured phycocyanin based on regression models developed for Zone C. Regression-estimated concentrations likely are more indicative of seasonal patterns in algal biomass (as indicated by chlorophyll concentrations) and microcystin than discretely collected samples because regression-estimated data have a much higher temporal resolution. Based on regression estimates, algal biomass and microcystin concentrations at the Wakefield site steadily increased from May through August. After August, concentrations decreased but remained relatively high compared to May and June. Daily chlorophyll maxima were as much as 400 times higher than daily minima, and daily microcystin maxima were as many as several orders of magnitude higher than daily minima. The extreme variability in algal biomass and microcystin concentrations at the Wakefield site reflects the development and dissipation of blooms, as indicated by the time-lapse cameras.

Based on regression-estimated microcystin concentrations, the KDHE watch and warning thresholds for microcystin were exceeded during mid-June through late November. Exceedance of KDHE advisory thresholds often changed from no advisory to watch or warning over the course of the day because of the variability in algal biomass and microcystin concentrations caused by bloom development and dissipation. Continuous water-quality monitors may be useful in informing public-health decisions in lakes with variable CyanoHAB conditions; however, site-specific models need to be developed, and best practices for using continuous water-quality monitors to inform CyanoHAB management strategies need to be established.

Spatial data were collected on May 26, July 21, and September 15, 2016, using a combination of a boat-mounted array and discrete water-quality samples analyzed for phytoplankton community composition and chlorophyll and microcystin concentrations. Spatial patterns were described using regression-estimated chlorophyll and microcystin concentrations. During the May 26, 2016, spatial surveys, cyanobacterial abundances were relatively low throughout Zone C and did not exceed KDHE guidance values compared to spatial surveys on July 21 and September 15. Regression-estimated chlorophyll concentrations were indicative of higher algal biomass uplake in Zone C, and decreases in the downlake direction towards Zone B. Regression-estimated chlorophyll concentrations also were more variable uplake than downlake. Based on regression estimates, microcystin concentrations did not exceed KDHE guidance values anywhere in Zone C on May 26. Spatial patterns in microcystin throughout Zone C did not match patterns in regression-estimated chlorophyll concentrations, likely because the algal community was not dominated by cyanobacteria at most locations in May.

During the July 21, 2016, spatial surveys, cyanobacterial abundances in Zone C exceeded KDHE guidance values in 50 percent of samples. The algal community in Zone C was dominated by cyanobacteria at all locations except two, where cyanobacteria codominated with diatoms. Both locations where cyanobacteria and diatoms codominated were north of the causeway. Regression-estimated chlorophyll concentrations were indicative of higher algal biomass north of the causeway and on the eastern shore of Zone C. On July 21, algal biomass did not always decrease in the downlake direction. There was a decrease just south of the causeway but an increase shortly after with higher concentrations into Zone B. Spatial maps indicated changes in algal distribution at a 0.5-meter depth, with algae moving to the central part of the lake north of the causeway and along the eastern shore south of the causeway. Most regression-estimated microcystin concentrations on July 21 exceeded KDHE guidance values, reflecting the pervasive bloom conditions in Zone C during this period. Spatial patterns in regression-estimated microcystin concentrations throughout Zone C were similar to patterns seen in discrete samples and regression-estimated chlorophyll concentrations, with higher concentrations north of the causeway and on the east shore of Zone C.

During the September 15, 2016, spatial surveys, cyanobacterial abundances did not exceed KDHE guidance values. The algal community north of the causeway was dominated by diatoms. The algal community throughout the rest of Zone C was dominated by cyanobacteria. Of regression-estimated microcystin concentrations on September 15, 80 percent did not exceed KDHE guidance values. Spatial patterns indicated northward movement of the cyanobacterial bloom consistent with a wind shift noted the previous day. On September 14, winds were generally from the north to northwest, shifting to the south by September 15. There was a northward progression of chlorophyll and microcystin during the spatial surveys. These data, along with the camera data and spatial and wind data from May and July, indicate that wind can be a major driver of the spatial and temporal variability of cyanobacterial blooms in Milford Lake and likely plays a role in the extent and duration of near-shore accumulations.

GPS tracking data reveals daily spatio-temporal movement patterns of waterfowl

Released March 05, 2019 10:18 EST

2019, Movement Ecology (7) 1-17

Fiona McDuie, Michael L. Casazza, Cory T. Overton, Mark P. Herzog, Christopher Hartman, Sarah H. Peterson, Cliff L. Feldheim, Joshua T. Ackerman


Spatio-temporal patterns of movement can characterize relationships between organisms and their surroundings, and address gaps in our understanding of species ecology, activity budgets, bioenergetics, and habitat resource management. Highly mobile waterfowl, which can exploit resources over large spatial extents, are excellent models to understand relationships between movements and resource usage, landscape interactions and specific habitat needs.


We tracked 3 species of dabbling ducks with GPS-GSM transmitters in 2015–17 to examine fine-scale movement patterns over 24 h periods (30 min interval), dividing movement pathways into temporally continuous segments and spatially contiguous patches. We quantified distances moved, area used and time allocated across the day, using linear and generalized linear mixed models. We investigated behavior through relationships between these variables.


Movements and space-use were small, and varied by species, sex and season. Gadwall (Mareca strepera) generally moved least (FFDs: 0.5–0.7 km), but their larger foraging patches resulted from longer within-area movements. Pintails (Anas acuta) moved most, were more likely to conduct flights > 300 m, had FFDs of 0.8–1.1 km, used more segments and patches per day that they revisited more frequently, resulting in the longest daily total movements. Females and males differed only during the post-hunt season when females moved more. 23.6% of track segments were short duration (1–2 locations), approximately 1/3 more than would be expected if they occurred randomly, and were more dispersed in the landscape than longer segments. Distance moved in 30 min shortened as segment duration increased, likely reflecting phases of non-movement captured within segments.


Pacific Flyway ducks spend the majority of time using smaller foraging and resting areas than expected or previously reported, implying that foraging areas may be highly localized, and nutrients obtainable from smaller areas. Additionally, movement reductions over time demonstrates behavioral adjustments that represent divergent energetic demands, the detection of which is a key advantage of higher frequency data. Ducks likely use less energy for movement than currently predicted and management, including distribution and configuration of essential habitat, may require reconsideration. Our study illustrates how fine-scale movement data from tracking help understand and inform various other fields of research.

Geology and assessment of undiscovered oil and gas resources of the Vilkitskii Basin Province, 2008

Released March 05, 2019 09:49 EST

2019, Professional Paper 1824-Z

Kenneth J. Bird, David W. Houseknecht, Janet K. Pitman

Thomas E. Moore, Donald L. Gautier, editor(s)

The Vilkitskii Basin is a separate petroleum province that lies beneath the continental shelf of the East Siberian Sea east of the New Siberian Islands and northwest of Wrangel Island. It is a basin known only on the basis of gravity data and three seismic profiles. A small, southern part of the basin overlies the Brooks Range–Chukotka late Mesozoic-early Paleogene orogenic belt, but most of the basin lies north of that belt. Its regional setting suggests that it may have similarities to other post-orogenic (successor) basins on the East Siberian Shelf as well as to foreland, rift-sag, and passive margin basins lying north of the orogenic belt such as the North Slope, North Chukchi and Podvodnikov Basins.

Although the basin’s petroleum potential is poorly known, extremely thick sediments, diapiric structures, and gas plumes interpreted from a seismic profile are considered favorable features for petroleum presence and imply that there may be an active petroleum system. An overall probability of about 30 percent of at least one petroleum accumulation >50 MMBOE (million barrels of oil equivalent) was determined based on estimated probabilities of the occurrence of petroleum source, adequate reservoir, trap and seal, and favorable timing. A single assessment unit (AU) was defined and assessed, resulting in mean estimates of undiscovered, technically recoverable resources that include about 100 million barrels of oil and 5,500 billion cubic feet of nonassociated gas.

Two-dimensional seismic velocities and structural variations at three British Columbia Hydro and Power Authority (BC Hydro) dam sites, Vancouver Island, British Columbia, Canada

Released March 05, 2019 09:23 EST

2019, Open-File Report 2019-1015

Rufus D. Catchings, Kofi O. Addo, Mark R. Goldman, Joanne H. Chan, Robert R. Sickler, Coyn J. Criley


In June, 2017, we acquired seismic data along five linear profiles at three British Columbia Hydro and Power Authority (BC Hydro, a Canadian provincial Crown Corporation) dam sites (John Hart, Ladore, and Strathcona Dams) on Vancouver Island, British Columbia, Canada. We also attempted to acquire linear seismic profiles at two additional BC Hydro dam sites (Ruskin Dam and Stave Falls Dam) east of the City of Vancouver, British Columbia, Canada; however, due to a seismograph programming error, little active-source data from Ruskin Dam and Stave Falls Dam were recorded. Thus, results from Ruskin Dam and Stave Falls Dam are not included in this report. At the three dam sites with successful data acquisition, we acquired both active- and passive-source data. Data acquisition details for each of the three dam sites varied in terms of seismic sources, the number of seismographs, and profile length and orientation. However, for active-source acquisition at each dam site, we acquired one or more linear seismic profiles ranging in length from about 150 to 400 meters (m), and along each profile, seismograph spacing was either 3 m or 5 m (see appendix 1). All data were recorded in three components (vertical and two horizontals). To greatly increase the resolution of the seismic velocity structure along these profiles, we co-located active sources at each seismograph.

Modelling for catchment management

Released March 04, 2019 16:41 EST

2019, Book chapter, Lake restoration handbook

Aroon Parshotam, Dale M. Robertson

David P. Hamilton, Kevin J. Collier, John M. Quinn, Clive Howard-Williams, editor(s)

Catchment models are useful tools to help describe and quantify the sources, transport, and fate of sediment, nutrients, and other constituents in a landscape. Results from catchment models are used to quantify and understand existing conditions and used in restoration efforts by defining areas with highest contributions (hotspots, where actions would be most beneficial) and describing the relative importance of various sources (what types of actions would be most beneficial). In practice, a continuum of models exists from simple empirical models to complex process-driven models, each requiring different types and amounts of information. Each of these models has its strengths and weaknesses, which should be considered when deciding which model to apply to a specific area. In many applications, a combination of models can be either coupled or run in series to help describe how nutrients and sediment are transported from the field to downstream receiving water bodies. In this chapter, we describe the continuum of catchment models that exist and provide information for choosing specific models for various management applications. We then provide examples of catchment models used to address a wide range of scientific and policy driven issues: two models commonly applied in New Zealand (CLUES and GLEAMS) and one model (SPARROW) applied to a large river basin in the United States (Mississippi River Basin).

Patterns of big sagebrush plant community composition and stand structure in the western United States

Released March 04, 2019 15:41 EST

2019, Rangeland Ecology and Management

Victoria E. Pennington, John B. Bradford, Kyle A. Palmquist, Rachel R. Renne, William K. Lauenroth

Big sagebrush (Artemisia tridentata Nutt.) plant communities are found in western North America and comprise a mix of shrubs, forbs, and grasses. Climate, topography, and soil water availability are important factors that shape big sagebrush stand structure and plant community composition; however, most studies have focused on understanding these relationships at sites in a small portion of the big sagebrush region. Our goal was to characterize detailed stand structure and plant composition patterns and identify environmental variables related to those patterns by sampling 15 sites distributed across the western United States. In each site, we characterized stand structure at the individual shrub level and at the site level. We quantified size distributions and assessed relationships among canopy volume, age, and height. We also characterized functional type cover and species composition and related those to climatic, topographic, and edaphic variables. Mean big sagebrush age ranged from 21 (± 8) to 57 (± 22) yr at individual sites, mean height ranged from 0.23 (± 0.12) to 0.67 (± 0.23) m, and mean canopy volume ranged from 0.03 (± 0.04) to 0.62 (± 0.51) m3. Bare ground and litter contributed the most cover (mean = 64%), followed by big sagebrush (mean = 39% of vascular plant cover). There was a negative relationship between big sagebrush cover and grass and forb cover. Species composition was related to both climate and elevation, likely because these variables influence water availability. Although our study was limited to 15 field sites, our detailed descriptions of widely distributed sites provide insight into the magnitude of variability in big sagebrush plant community structure.

Trends in landbird density at two national parks in fragmented, mixed-use landscapes of the Pacific Northwest

Released March 04, 2019 15:39 EST

2019, Northwestern Naturalist (100) 1-25

Chris Ray, Mandy Holmgren, Robert L. Wilkerson, Rodney B. Siegel, John R. Boetsch, Kurt J. Jenkins, Jason I. Ransom

M. Holmgren, R. Wilkerson, R. Siegel, J. Ransom, Kurt J. Jenkins, J. Boetsch, editor(s)

National parks play a key role in conserving species by providing landscapes where threats from anthropogenic disturbance are reduced. In a recent study of 3 large wilderness parks in the Pacific Northwest, nearly all landbird species were found to be stable or increasing. Nonetheless, contemporary results from the Breeding Bird Survey and mark-recapture studies fuel concerns that some landbirds in the Pacific Northwest are trending in sync with many North America species in widespread decline. Although landbird populations might be thriving in large parks with extensive old-growth forest, those in smaller parks with less intact wilderness and higher ratios of edge-to-interior habitat might reflect the stressors inherent in more human-dominated landscapes. We conducted landbird point-count surveys from 2005 to 2016 in 2 national historical parks situated in the more human-dominated landscapes of this region, San Juan Island National Historical Park and Lewis and Clark National Historical Park. Established primarily to protect cultural resources, these parks lack old-growth forest and consist of relatively small parcels embedded in fragmented, multi-use landscapes. Here, we apply recent developments in point-count analysis to estimate trends in population density for 50 landbird species commonly detected in these small parks, including lagged effects of precipitation and temperature on the annual density of each species, and effects of survey conditions on species detection. All but 3 species exhibited stable densities in both parks, and more than half of the populations analyzed clearly increased in density over the study period. Notable exceptions were single-park declines in Olive-sided Flycatcher (Contopus cooperi), Northern Flicker (Colaptes anratus), and Hutton's Vireo (Vireo huttoni). Annual variation in population density was often related to climate, with generally positive responses to a recent deficit in annual precipitation-as-snow, and more variable responses to higher mean spring temperature. These results reinforce trends estimated for 3 large national parks in the Pacific Northwest, suggesting recent stability of landbird populations in parks of this region, independent of park size or setting.

Physical, biogeochemical, and meteorological factors responsible for interannual changes in cyanobacterial community composition and biovolume over two decades in a eutrophic lake

Released March 04, 2019 15:28 EST

2019, Hydrobiologia (828) 165-182

Chelsea A. Weirich, Dale M. Robertson, Todd R. Miller

This study used a 20-year dataset (1995–2014) to identify factors affecting cyanobacterial community composition (CCC) and abundance in a eutrophic lake. We hypothesized that differences in thermal structure, nutrients, and meteorology drive interannual variability in CCC and abundance. Cluster analysis differentiated dominant cyanobacteria into rare, low abundance, or sporadically occurring taxa. The bloom-forming genera were Microcystis and Aphanizomenon, accounting for ~ 70% of total cyanobacterial biovolume (BV) on average, whereas unusually high abundance of Planktothrix, Synechococcus, and Oscillatoria were clear outliers in three of the years. Variability in CCC was significantly correlated (P < 0.05, R > 0.3) with ice duration, Kjeldahl nitrogen (TKN), and spring nitrite + nitrate (NO2+3); ice duration and TKN were associated with the occurrence of primarily non-bloom-forming genera. Pairwise correlations tested linear, exponential, and polynomial correlates of absolute and relative total Cyanophyta, Microcystis, or Aphanizomenon BV. TKN, total nitrogen (TN) and phosphorus (TP), TN:TP ratio, Schmidt stability, and rainfall correlated with total Cyanophyta, Microcystis, and Aphanizomenon BV, whereas ice cover, NO2+3, and TKN correlated with relative Microcystis and Aphanizomenon BV. Despite increasing TN:TP ratio over two decades, cyanobacterial abundance had not changed significantly. These data suggest differing responses of cyanobacterial genera to important environmental factors over two decades.

Isotopic and petrologic investigation, and a thermomechanical model of genesis of large-volume rhyolites in arc environments: Karymshina Volcanic Complex, Kamchatka, Russia

Released March 04, 2019 15:25 EST

2019, Frontiers in Earth Science (6) 1-27

Ilya N. Bindeman, Vladimir L. Leonov, Dylan P. Colòn, Aleksey N. Rogozin, Niccole Shipley, Brian Jicha, Matthew W. Loewen, Taras V. Gerya

The Kamchatka Peninsula of eastern Russia is currently one of the most volcanically active areas on Earth where a combination of >8 cm/yr subduction convergence rate and thick continental crust generates large silicic magma chambers, reflected by abundant large calderas and caldera complexes. This study examines the largest center of silicic 4-0.5 Ma Karymshina Volcanic Complex, which includes the 25 × 15 km Karymshina caldera, the largest in Kamchatka. A series of rhyolitic tuff eruptions at 4 Ma were followed by the main eruption at 1.78 Ma and produced an estimated 800 km3 of rhyolitic ignimbrites followed by high-silica rhyolitic post-caldera extrusions. The postcaldera domes trace the 1.78 Ma right fracture and form a continuous compositional series with ignimbrites. We here present results of a geologic, petrologic, and isotopic study of the Karymshina eruptive complex, and present new Ar-Ar ages, and isotopic values of rocks for the oldest pre- 1.78 Ma caldera ignimbrites and intrusions, which include a diversity of compositions from basalts to rhyolites. Temporal trends in δ18O, 87Sr/86Sr, and 144Nd/143Nd indicate values comparable to neighboring volcanoes, increase in homogeneity, and temporal increase in mantle-derived Sr and Nd with increasing differentiation over the last 4 million years. Data are consistent with a batholithic scale magma chamber formed by primarily fractional crystallization of mantle derived composition and assimilation of Cretaceous and younger crust, driven by basaltic volcanism and mantle delaminations. All rocks have 35–45% quartz, plagioclase, biotite, and amphibole phenocrysts. Rhyolite-MELTS crystallization models favor shallow (2 kbar) differentiation conditions and varying quantities of assimilated amphibolite partial melt and hydrothermally-altered silicic rock. Thermomechanical modeling with a typical 0.001 km3/yr eruption rate of hydrous basalt into a 38 km Kamchatkan arc crust produces two magma bodies, one near the Moho and the other engulfing the entire section of upper crust. Rising basalts are trapped in the lower portion of an upper crustal magma body, which exists in a partially molten to solid state. Differentiation products of basalt periodically mix with the resident magma diluting its crustal isotopic signatures. At the end of the magmatism crust is thickened by 8 km. Thermomechanical modeling show that the most likely way to generate large spikes of rhyolitic magmatism is through delamination of cumulates and mantle lithosphere after many millions of years of crustal thickening. The paper also presents a chemical dataset for Pacific ashes from ODDP 882 and 883 and compares them to Karymshina ignimbrites and two other Pleistocene calderas studied by us in earlier works.

Influenza A prevalence and subtype diversity in migrating teal sampled along the United States Gulf Coast

Released March 04, 2019 15:18 EST

2019, Avian Diseases

Deborah Carter, Paul T. Link, Patrick Walther, Andrew M. Ramey, David E. Stallknecht, Rebecca L. Poulson

Wild birds in the order Anseriformes are important reservoirs for influenza A viruses (IAV); however, IAV prevalence and subtype diversity may vary by season, even at the same location. To better understand the ecology of IAV during waterfowl migration through the Gulf Coast of the United States (Louisiana and Texas), surveillance of blue-winged (Spatula discors) and American green-winged (Anas carolinensis) teal was conducted annually during the spring (live-capture; 2012-2017) and fall (hunter-harvested; 2007-2017) at times inferred to coincide with northward and southward movements, respectively, for these waterfowl species. During spring migration, 266 low pathogenicity (LP) IAV positive samples were recovered from 7,547 paired cloacal/oropharyngeal (COP) samples (prevalence: 3.5%; annual range: 1.3%-8.4%). During fall migration, 650 LP IAV positive samples were recovered from 9,493 COP samples (prevalence: 6.8%; annual range: 0.4%-23.5%). Overall, 34 and 20 different IAV subtypes were recovered during fall and spring sampling, respectively. Consistent with previous results for fall migrating ducks, H3 and H4 HA subtypes were most common; however, H4 subtype viruses predominated every year. This is in contrast to the predominance of LP H7 and H10 HA subtype viruses in both species during spring. The N6 and N8 NA subtypes, which were usually associated with H4, were most common during fall; the N6 subtype was not recovered in the spring. These consistent seasonal trends in IAV subtype detection in both species are currently not understood and highlight the need for further research regarding potential drivers of spatiotemporal patterns of infection such as population immunity.

U.S. Geological Survey—Northern Prairie Wildlife Research Center 2017 research activity report

Released March 04, 2019 11:44 EST

2019, Circular 1451

Mark H. Sherfy, editor(s)

The mission of Northern Prairie Wildlife Research Center is to provide scientific information needed to conserve and manage the Nation’s natural capital for current and future generations, with an emphasis on migratory birds, Department of the Interior trust resources, and ecosystems of the Nation’s interior.  This report provides an overview of the studies conducted at Northern Prairie during fiscal year 2017 in pursuit of this mission.  Studies are organized under a framework developed by the U.S. Geological Survey Ecosystems Mission Area, identifying primary and secondary alignment with focal areas of research, and summarizing recent scientific products resulting from these studies.  Partnerships with Federal, State, and non-Governmental organizations are essential to a robust program of applied ecological research, and we thank our many collaborators and colleagues whose contributions made this work possible. 

Climate change effects on deer and moose in the midwest

Released March 04, 2019 10:38 EST

2019, Journal of Wildlife Management

Sarah R. Weiskopf, Olivia E. LeDee, Laura M. Thompson

Climate change is an increasing concern for wildlife managers across the United States and Canada. Because climate change may alter populations and harvest dynamics of key species in the region, midwestern states have identified the effects of climate change on ungulates as a priority research area. We conducted a literature review of projected climate change in the Midwest and the potential effects on white‐tailed deer (Odocoileus virginianus) and moose (Alces alces). Warmer temperatures and decreasing snowpack in the region favor survival of white‐tailed deer. In contrast, moose may become physiologically stressed in response to warming, and increasing deer populations spreading disease will exacerbate the problem. Although there is some uncertainty about exactly how the climate will change, and to what degree, robust projections suggest that deer populations will increase in response to climate change and moose populations will decrease. Managers can begin preparing for these changes by proactively creating management plans that take this into account.

The plant diversity sampling design for The National Ecological Observatory Network

Released March 04, 2019 10:31 EST

2019, Ecosphere (10) 1-18

David T. Barnett, Peter B. Adler, Benjamin R. Chemel, Paul A. Duffy, Brian J. Enquist, James B. Grace, Susan P. Harrison, Robert K. Peet, David S. Schimel, Thomas J. Stohlgren, Mark Vellend

The National Ecological Observatory Network (NEON) is designed to facilitate an understanding of the impact of environmental change on ecological systems. Observations of plant diversity—responsive to changes in climate, disturbance, and land use, and ecologically linked to soil, biogeochemistry, and organisms—result in NEON data products that cross a range of organizational levels. Collections include samples of plant tissue to enable investigations of genetics, plot‐based observations of incidence and cover of native and non‐native species, observations of plant functional traits, archived vouchers of plants, and remote sensing airborne observations. Spatially integrating many ecological observations allows a description of the relationship of plant diversity to climate, land use, organisms, and substrates. Repeating the observations over decades and across the United States will iteratively improve our understanding of those relationships and allow for the testing of system‐level hypotheses as well as the development of predictions of future conditions.

Heat and mass transport in a vapor-dominated hydrothermal area in Yellowstone National Park, USA: Inferences from magnetic, electrical, electromagnetic, subsurface temperature and diffuse CO2 flux measurements

Released March 04, 2019 10:29 EST

2019, Journal of Geophysical Research B: Solid Earth (124) 291-309

Claire Bouligand, Shaul Hurwitz, Jean Vandemeulebrouck, Svetlana Byrdina, Mason A. Kass, Jennifer L. Lewicki

Vapor‐dominated hydrothermal systems are characterized by localized and elevated heat and gas flux. In these systems, steam and gas ascend from a boiling water reservoir, steam condenses beneath a low‐permeability cap layer, and liquid water descends, driven by gravity (“heat pipe” model). We combine magnetic, electromagnetic, and geoelectrical methods and CO2 flux and subsurface temperature measurements in the Solfatara Plateau Thermal Area in the Yellowstone Caldera to address several fundamental questions: (1) What are the structural and/or lithological controls on heat and mass transport in vapor‐dominated areas? (2) What is the geometry and size of convecting multiphase thermal plumes? (3) Are thermal plumes associated with subsurface rock alteration and demagnetization? Magnetic and electromagnetic data inversions suggest an asymmetric 50‐ to 100‐m thick basin of glacial deposits with the thickest part adjacent to the margin of a rhyolite flow. The 3‐D electrical conductivity model in the glacial basin reveals a narrow vertical conductor interpreted as a focused multiphase plume, which coincides at the ground surface with the heat and CO2 flux maxima. The magnetic data suggest that destruction of magnetic minerals due to rock alteration associated with the hydrothermal plume occurs mainly near the ground surface. We propose a model where the buoyant multiphase plume forms in response to decompression, boiling, and phase separation of pressurized thermal groundwater that discharges from the brecciated base of a rhyolite flow into the basin of glacial deposits. Results from multiphase groundwater flow and heat transport numerical simulations corroborate the first‐order characteristics of this model.

Assessment of Columbia and Willamette River flood stage on the Columbia Corridor Levee System at Portland, Oregon, in a future climate

Released March 04, 2019 10:11 EST

2019, Scientific Investigations Report 2018-5161

Susan A. Wherry, Tamara M. Wood, Hans R. Moritz, Keith B. Duffy

To support Levee Ready Columbia’s (LRC’s) effort to re-certify levees along the Columbia and Willamette Rivers and remain accredited, two 2-dimensional hydraulic models, Adaptive Hydraulics and Delft3D-Flexible Mesh, were used to simulate the effects of plausible extreme high water during the 2030 to 2059 period. The Columbia River was simulated from Bonneville Dam, situated at river mile (RM) 145, to the mouth of Columbia River, and the Willamette River was simulated from Willamette Falls, RM 26.2, to the Columbia River confluence. Inputs to the models included light detection and ranging (lidar) and bathymetric mapping data to determine bed level, and boundary conditions in the form of daily inflow hydrographs and water levels in the ocean offshore of the mouth of the Columbia River.

Future conditions were based on climate science data developed by the U.S. Army Corps of Engineers and others. These conditions included future streamflow and coastal ocean water levels. The hypothetical, extreme but plausible, upstream boundary was based on scaling up the hydrographs from the 1996 flood. Scaling factors were determined by comparing the peak flow rankings determined from flood frequency analyses of historical unregulated periods and 2040s simulated unregulated winter streamflow. The comparison resulted in scaling up the Columbia River hydrograph by 40-percent and scaling up the Willamette River and Lower Columbia River tributaries hydrographs by 20-percent. The downstream ocean boundary was based on a combination of sea-level change, high tide, and storm surge.

The models were calibrated for two historical periods: (1) from January 15 to February 28, 1996, and (2) from April 12 to July 12, 1997. The two models compared well to the measured water-surface elevation over the historical periods and had good performance statistics, with root-mean square error ranging from 0.085 to 0.32 meters, Nash-Sutcliffe values greater than 0.96, and bias ranging from -0.03 to 0.28 meters. The simulated peak stage in the Columbia River at Vancouver, Washington, for 1996 was 9.60 and 9.98 meters (31.5 and 32.7 feet) compared to the measured peak of 9.89 meters (32.5 feet). Future peak stage then was simulated with boundary conditions representing extreme but plausible future conditions at the inflow sites and the ocean boundary.

The two calibrated models compared well in their simulations of extreme but plausible future conditions. For the 0-meter sea-level change scenario, the simulated peak stage in the Columbia River at Vancouver was 11.15 and 11.39 meters (36.6 and 37.4 feet); and for the 1-meter sea-level change scenario, the simulated peak stage in the Columbia River was 11.25 and 11.54 meters (36.9 and 37.9 feet). The total increase in stage as compared to the 1996 measured peak stage ranged from 1.26 to 1.65 meters (4.13 to 5.40 feet).

Arizona hedgehog cactus (Echinocereus triglochidiatus var. arizonicus)—A systematic data assessment in support of recovery

Released March 04, 2019 08:50 EST

2019, Open-File Report 2019-1004

Kathryn A. Thomas, Daniel F. Shryock, Todd C. Esque

The Arizona hedgehog cactus (Echinocereus triglochidiatus var. arizonicus) is endemic to central Arizona in Gila and Pinal Counties, and has been federally listed as endangered by the U.S. Fish and Wildlife Service (FWS) since 1979. Mining, mineral exploration, and highway development have resulted in habitat degradation and loss of individual plants. Therefore, decreases in the population of the cactus are expected to continue. In response to a request from FWS to compile, evaluate, and synthesize data for the cactus, we identified and evaluated existing survey and monitoring data for the cactus and conducted a demographic analysis with suitable data.

Systematic surveys for the Arizona hedgehog cactus did not begin until the late 1970s. Early surveys generally were anecdotal descriptions of cactus populations and precisely georeferenced records of individual cactus occurrence did not occur until global positioning systems were widely used. Much of the georeferenced data have been collected by consultants for mining operations, the Arizona Department of Transportation, the U.S. Forest Service, and independent surveyors. Occurrence records have been compiled by the Arizona Game and Fish Department Heritage Data Management System, but submission of these data may be incomplete, and the attributes reported have varied among the contributing entities. The compilation and management of survey data is essential for field-based evidence of the size, distribution, and range extent of the cactus. In support of consistency in future survey data collection, this report makes several suggestions for future surveys.

Monitoring for the Arizona hedgehog cactus, defined as repeat observations of the status of cactus individuals, has been done by consulting companies for three mines. Demographic monitoring further involves marking individual cacti in consistently defined plots and recording the fate of each cacti through time, including birth, growth, reproduction, and death. We were able to use demographic monitoring data provided by two consulting companies to calculate survival and population growth rates, using several statistical approaches. Resulting models indicate that larger cacti, as measured by their number of stems, have greater survival rates. Larger individuals also had higher probability of producing more flowers. Small cacti had the lowest survivorship, with potentially only 15–20 percent reaching large size. Most populations monitored by the two companies were stable to increasing. However, there were differences in the growth rates among plots and some plots had negative population growth rates. The demographic monitoring data we used represented relatively dense populations of undisturbed cacti. Hence, overall positive population growth rates were not influenced by any large-scale disturbances. Previous analyses with cacti and other species suggest that more than 10 years of data are necessary to accurately forecast long-term population trajectories. As the monitoring intervals we evaluated were shorter, they represent short-term dynamics only. Several suggestions are made in the report to improve collection of monitoring data to support evidence-based estimates of demographic characteristics of the Arizona hedgehog cactus.

Influence of salinity on relative density of American crocodiles (Crocodylus acutus) in Everglades National Park: Implications for restoration of Everglades ecosystems

Released March 02, 2019 14:37 EST

2019, Ecological Indicators (102) 608-616

Frank J. Mazzotti, Brian Smith, Michiko Squires, Michael S. Cherkiss, Seth C Farris, Caitlin Hackett, Kristen M. Hart, Venetia Briggs-Gonzalez, Laura A. Brandt

The status of the American crocodile (Crocodylus acutus) has long been a matter of concern in Everglades National Park (ENP) due to its classification as a federal and state listed species, its recognition as a flagship species, and its function as an ecosystem indicator. Survival and recovery of American crocodiles has been linked with regional hydrological conditions, especially freshwater flow to estuaries, which affect water levels and salinities. We hypothesize that efforts to restore natural function to Everglades ecosystems by improving water delivery into estuaries within ENP will change salinities and water levels which in turn will affect relative density of crocodiles. Monitoring ecological responses of indicator species, such as crocodiles, with respect to hydrologic change is necessary to evaluate ecosystem responses to restoration projects. Our objectives were to monitor trends in crocodile relative density within ENP and to determine influences of salinity on relative density of crocodiles. We examined count data from 12 years of crocodile spotlight surveys in ENP (2004 to 2015) and used a hierarchical model of relative density that estimated relative density with probability of detection. The mean predicted value for relative density (λ) across all surveys was 2.9 individuals/km (95% CI: 2.0 – 4.2); relative density was estimated to decrease with increases in salinity. Routes in ENP’s Flamingo/Cape Sable area had greater crocodile relative density than routes in the West Lake/Cuthbert Lake area and Northeast Florida Bay areas. These results are consistent with the hypothesis that restored flow and lower salinities will result in an increase in crocodile population size and provide support for the ecosystem management recommendations for crocodiles, which currently are to restore more natural patterns of freshwater flow to Florida Bay. Thus, monitoring relative density of American crocodiles will continue to be an effective indicator of ecological response to ecosystem restoration.

Cooperative Fish and Wildlife Research Units program—2018 year in review

Released March 01, 2019 17:00 EST

2019, Circular 1452

John F. Organ, John D. Thompson, Dawn E. Childs, Donald E. Dennerline

The Cooperative Fish and Wildlife Research Units (CRU) program had an interesting and challenging year in 2018. We made significant strategic advances on many fronts and had setbacks in others.

Our relationship with the U.S. Fish and Wildlife Service, the agency we belonged to from 1935 to the mid-1990s, was further reinforced through strategic efforts with the Service’s Science Applications senior staff. This is bearing fruit in terms of research collaborations and funding support. As part of a larger effort between the U.S. Geological Survey (USGS) Ecosystems Mission Area and the Service’s endangered species program, we are also collaborating to address science needs for species in pre-listing status. Barry Grand, Unit Supervisor (South), has been instrumental in this effort.

Tom Edwards of the Utah Unit has met with representatives of the U.S. Fish and Wildlife Service and the Association of Fish and Wildlife Agencies to promote training of leaders and “hands dirty” biologists in species distribution modeling. The Association passed a unanimous resolution endorsing the training at their midyear meeting in March. Tom held a workshop at the annual meeting of the Association of Fish and Wildlife Agencies in September, and future workshops, supported by the U.S. Fish and Wildlife Service, will be held bringing State agency and U.S. Fish and Wildlife Service biologists together to work on species of common concern.

Wyoming Unit Leader Matt Kauffman’s pioneering work in identifying and mapping big-game migration corridors has captured the attention of conservationists far and wide. In the spring, the Secretary of the Interior signed Secretarial Order No. 3362, "Improving Habitat Quality in Western Big-Game Winter Range and Migration Corridors" directing efforts of several U.S. Department of the Interior (DOI) bureaus to collaborate with States in identifying and protecting big-game corridors in 11 States. Matt has conducted several workshops that directly support the Secretarial order, and more are planned. Corridor mapping efforts supported by the USGS and the DOI, based in the States and coordinated by Matt, are unfolding.

Unit Administrative Officer Shana Coulby and her staff hosted a training program for university support staff at USGS National Headquarters in March. Shana’s team did a superb job, and the camaraderie among all was evident.

We co-sponsored the third in a series of workshops at the North American Wildlife and Natural Resources Conference in March on bridging the gap between science and management.

The State Department requested that we coordinate a workshop that would bring CRU scientists and other U.S. representatives together with Brazilian, Colombian, and Peruvian scientists and decision makers to develop best practices to minimize environmental damage from infrastructure development in the Amazon and to collaborate on science needs. The workshop was held in Iquitos, Peru, in the heart of the Amazon during August.

Our cooperator community, represented by the National Cooperators Coalition, was very active in response to the President’s budget proposal that would have redirected funding for the CRU program to other priorities. Their efforts are reflected in the House and Senate marks on the fiscal year 2019 budget that not only restored funding, but recommended increases.

You will see in this report many other accomplishments of our individual scientists and students during 2018. It was an impressive and productive year! What you won’t see chronicled is the work of the CRU headquarters staff and University support staff. These folks are extraordinary in their dedication to working with cooperators and scientists to solve problems and ensure the important work gets accomplished with minimal interference. We are truly fortunate to have such skilled and dedicated folks in the trenches.

I was fortunate to visit several units during 2018. For me, this is the most enriching part of my duties. I get to see firsthand the work our scientists do, the incredible students being mentored, and meet our cooperators on their turf.

As we look forward towards the horizon, 2019 looks brighter for the CRU program. Efforts by our cooperators to generate support for filling our vacancies are materializing. Our cadre of scientists is second to none, and the breadth and depth of our work are nothing short of impressive. Thanks to all who are part of this cooperative endeavor—conservation is the ultimate winner in our efforts!

Cooperative Fish and Wildlife Research Units program—2018 year in review postcard

Released March 01, 2019 17:00 EST

2019, General Information Product 187

John F. Organ, John D. Thompson, Dawn Childs, Donald E. Dennerline

This postcard provides details about the "Cooperative Fish and Wildlife Research Units Program—2018 Year in Review," U.S. Geological Survey Circular 1452, now available at https://doi.org/10.3133/cir1452. In this report, you will find details about the Cooperative Fish and Wildlife Research Units (CRU) program relating to its background, fish and wildlife science, students, staffing, vacancies, research funding, outreach and training, science themes, accolades, and professional services. You will see snapshots of CRU projects with information on how results have been or are being applied by cooperators. This is the essence of what we do: science that matters.

Throughout the year, keep up with CRU research projects at http://www.coopunits.org.

Geologic map of the Hartsel Quadrangle, Park County, Colorado

Released March 01, 2019 16:34 EST

2019, Open-File Report 17-04

Peter E. Barkmann, Karen J. Houck, Marieke Dechesne, Jonathan R. Lovekin, Erinn P. Johnson

The Hartsel quadrangle sits nearly in the center of the complex South Park Laramide structural basin. Generally, the basin can be described as an asymmetrical down-faulted feature, dipping to the east. It is bounded by two northwest-trending uplifts: the Sawatch uplift to the west and the Front Range uplift to the east. The west-verging Elkhorn thrust, which places Proterozoic intrusive and metamorphic rocks within the Front Range uplift over Phanerozoic sediments in the basin, passes just east of the quadrangle. Seismic data and deep oil and gas well logs indicate that a series of imbricate thrust faults extend west, and in front of, the Elk horn thrust fault. The Hartsel uplift is a westward-jutting structural salient of the Front Range uplift that brings Proterozoic rocks farther into the basin south of the town of Hartsel. The quadrangle also spans the late Paleozoic boundary between the central Colorado trough (DeVoto, 1972) to the west and Frontrangia (Mallory, 1958) to the east. The Neogene Rio Grande rift system lies to the west of South Park Basin in the upper Arkansas River valley. Examples of Neogene extension can be found throughout South Park, as described by Stark and others (1949), De Voto (1971), and Ruleman and others (2011). In addition, there is evidence of ongoing local deformation related to dissolution and possible collapse of Paleozoic evaporite deposits across much of the west side of the basin (Kirkham and others, 2012).

Adjudicating groundwater: A judge’s guide to understanding groundwater and modeling

Released March 01, 2019 12:54 EST

2019, Book

Thomas Harter, Tara Moran, Eric Wildman

Alf Brandt, Michael N. Fienen, Jeremy White, editor(s)

Dividing the Waters offers this groundwater science bench book that cannot be matched by any other scientific or judicial publication.  Adjudicating Groundwater combines the expertise and experience of academic scientists (UC Davis/Stanford), federal scientists (U.S. Geological Survey), and judicial officers to create a resource that can fulfill the needs of judges tackling the most difficult groundwater conflicts.  This bench book explains both the fundamentals of groundwater science (hydrogeology) and groundwater modeling.  The bench book received peer review from scientists and judges, with oversight by the U.S. Geological Survey, making this book among the most reliable resources for judges with water cases.

Water use in Louisiana, 2015

Released March 01, 2019 12:54 EST

2018, Water Resources Special Report 18

Angela Collier, B. Pierre Sargent

In 2015, approximately 8,720 million gallons per day (Mgal/d) of water was withdrawn from groundwater and surface-water sources in Louisiana, a 2.6 percent increase from 2010. Total groundwater withdrawals were about 1,750 Mgal/d, an increase of 12 percent from 2010, and total surface-water withdrawals were about 6,970 Mgal/d, an increase of 0.44 percent from 2010 to 2015.

Total water withdrawals, in Mgal/d, in 2015 for the various categories of use were as follows: public supply—715, industry—2,155, power generation—4,265, rural domestic—39, livestock—6, rice irrigation—825, general irrigation—225, and aquaculture—490. From 2010 to 2015, Louisiana’s total withdrawals for public supply decreased by 3.4 percent, industry increased by 5.7 percent, power generation decreased by 3.9 percent, rural domestic decreased by 4.1 percent, livestock decreased by 21 percent, rice irrigation increased by 20 percent, general irrigation decreased by 6.0 percent, and aquaculture increased by 58 percent.

About 48 percent (approximately 850 Mgal/d) of all groundwater withdrawn was from the Chicot aquifer system and 22 percent (approximately 385 Mgal/d) was withdrawn from the Mississippi River alluvial aquifer. Since 2010, withdrawals from the Chicot aquifer system increased by 30 percent and withdrawals from the Mississippi River alluvial aquifer decreased by 2.9 percent.

About 70 percent (4,905 Mgal/d) of all surface water withdrawn was from the Mississippi River mainstem. This value represents a 1.1-percent decrease in withdrawals from 2010 to 2015.

All water-withdrawal and water-use data presented in this report should be considered estimates. Because of rounding, totals and percentages presented in the tables, figures, and text in the report may differ slightly from totals or percentages calculated individually

Surficial materials of Massachusetts—A 1:24,000-scale geologic map database

Released March 01, 2019 11:30 EST

2018, Scientific Investigations Map 3402

The surficial materials geologic map database defines the distribution of nonlithified earth materials at the land surface in the 189 7.5-minute, 1:24,000-scale quadrangles that cover the Commonwealth of Massachusetts (index map). Across the State, these materials range in thickness from a few feet to more than 500 feet (ft). In some places, surficial materials are absent where bedrock is at the land surface. The geologic map database differentiates surficial materials of Quaternary age on the basis of their lithologic characteristics (such as grain size and sedimentary structures), constructional geomorphic features, stratigraphic relationships, and age. The mapped distribution of surficial materials defines the areas of exposed bedrock and the boundaries between glacial till, glacial stratified deposits, and overlying postglacial deposits at a 1:24,000-scale level of accuracy.

Most of the surficial materials in Massachusetts are deposits of the last two continental ice sheets that covered all of New England in the latter part of the Pleistocene ice age. The glacial deposits are divided into two broad categories, glacial till and moraine deposits, and glacial stratified deposits. Widespread till deposits were laid down directly on bedrock or on semi-consolidated coastal plain strata by glacier ice. Tills in thick-till (>15 ft thick) drumlin landforms are found in all parts of the State. Areas of shallow bedrock contain thin discontinuous till deposits and numerous bedrock outcrops, and are located chiefly in rocky upland areas. Moraine deposits related to glacial ice lobes of the last ice sheet are located mostly in southeastern Massachusetts. Glacial stratified deposits are concentrated in valleys and lowland areas and were laid down by glacial meltwater in streams, lakes, and the sea in front of the retreating ice margin during the last deglaciation. Postglacial deposits, primarily flood-plain alluvium and swamp deposits, make up a lesser proportion of the unconsolidated materials.

The geodatabase included with this report contains MapUnitPolys, MapUnitOverlayPolys, and OverlayPolys, which show the distribution of geologic units that cover the entire map area and are intended for use at quadrangle scale (1:24,000). These data layers can be clipped by quadrangle or by town boundary. Unlike the units in conventional geologic maps, the digitally defined MapUnitOverlayPolys are arranged in order according to superposition. The polygons for till and bedrock are on the bottom and are overlain by the succeeding stratified deposits; these materials are shown everywhere they occur, including beneath postglacial deposits such as swamp deposits, and also beneath water bodies. The postglacial deposits are on top because these materials overlie the other, older deposits. Instructions for using the digital files are included in the README file. A series of map figures in the pamphlet illustrates the stacking of geologic units in a portion of the Mount Toby quadrangle. The BaseMaps folder contains the 1:24,000-scale topographic base map images (1944–1977 editions) used for this compilation.

This report supersedes U.S. Geological Survey Open-File Reports 2006-1260-A, -B, -C, -D, -E, -F, -G, and -I.

Evidence for a duplicated mitochondrial region in Audubon’s shearwater based on MinION sequencing

Released March 01, 2019 11:25 EST

2019, Mitochondrial DNA Part A (30) 256-263

Lucas Torres, Andreanna J. Welch, Catherine Zanchetta, Terry Chesser, Maxime Manno, Cecile Donnadieu, Vincent Bretagnolle, Eric Pante

Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon’s shearwater) using the long-read MinION (ONT) technology. Two mitogenomes were assembled from the same individual, differing by 52 SNPs and in length. The shorter was 19 kb long while the longer was 21 kb, due to the presence of two identical copies of nad6, three tRNA, and two dissimilar copies of the control region (CR). Contrary to albatrosses, cobwas not duplicated. We further detected a complex repeated region of undetermined length between the CR and 12S. Long-read sequencing suggests heteroplasmy and a novel arrangement within the duplicated region, indicating a complex evolution of the mitogenome in Procellariiformes.

Practical tips to establish an actionable science portfolio for climate adaptation

Released March 01, 2019 11:21 EST

2019, Science and Public Policy (46) 148-153

Gustavo A. Bisbal

The delivery of climate adaptation science products and services to inform resource management decisions—otherwise known as actionable climate adaptation science—is the primary driver and intended outcome of the science portfolios administered within the Department of the Interior's Climate Adaptation Science Center (CASC) network in the USA. This commitment hinges on the essential requirement that natural and cultural resource managers (science users) and scientists (science producers) work in unison with one another. This partnership may be illustrated by the conventional demand and supply relationship, where resource managers create the demand term by explicitly describing a priori top decisions or priority actions concerning the natural or cultural resources they administer, and scientists supply relevant research products and services. But an ideal interaction of users and producers is not trivial and presents challenges in the process of establishing an actionable science portfolio. A few practical suggestions are presented here to set up a productive dialogue between resource managers and scientists, and broker that conversation as they work side-by-side toward agreed-upon common objectives. These useful tips stem from working towards the goal of establishing actionable science portfolios within the CASC network and may prove valuable to similar entities committed to delivering climate adaptation science to address resource management concerns.

Weak effects of geolocators on small birds: a meta‐analysis controlled for phylogeny and publication bias

Released March 01, 2019 11:19 EST

2019, Journal of Animal Ecology

Vojtěch Brlík, Jaroslav Koleček, Malcolm Burgess, Steffen Hahn, Diana Humple, Milos Krist, Janne Ouwehand, Emily L. Weiser, Peter Adamik, José A. Alves, Debora Arlt, Sanja Barišić, Detlef Becker, Eduardo J. Belda, Vaclav Beran, Christiaan Both, Susana P. Bravo, Martins Briedis, Chutný Bohumír, Davor Ćiković, Nathan W. Cooper, Joana S. Costa, Víctor R. Cueto, Tamara Emmenegger, Kevin Fraser, Olivier Gilg, Marina Guerrero, Michael T. Hallworth, Chris Hewson, Frédéric Jiguet, James Johnson, Tosha Kelly, Dmitry Kishkinev, Michel Leconte, Terje Lislevand, Simeon Lisovski, Cosme López, Kent P. McFarland, Peter P. Marra, Steven M. Matsuoka, Matyjasiak. Piotr, Christoph M. Meier, Benjamin Metzger, Juan S. Monrós, Roland Neumann, Amy Newman, Ryan Norris, Tomas Pärt, Václav Pavel, Noah Perlut, Markus Piha, Jeroen Reneerkens, Christopher C. Rimmer, Amélie Roberto-Charro, Chiara Scandolara, Natalia Sokolova, Makiko Takenaka, Dirk Tolkmitt, Herman van Oosten, Arndt H. J. Wellbrock, Hazel Wheeler, Jan van der Winden, Klaudia Witte, Brad Woodworth, Petr Procházka

Currently, the deployment of tracking devices is one of the most frequently used approaches to study movement ecology of birds. Recent miniaturisation of light‐level geolocators enabled studying small bird species whose migratory patterns were widely unknown. However, geolocators may reduce vital rates in tagged birds and may bias obtained movement data.

There is a need for a thorough assessment of the potential tag effects on small birds, as previous meta‐analyses did not evaluate unpublished data and impact of multiple life‐history traits, focused mainly on large species and the number of published studies tagging small birds has increased substantially.

We quantitatively reviewed 549 records extracted from 74 published and 48 unpublished studies on over 7,800 tagged and 17,800 control individuals to examine the effects of geolocator tagging on small bird species (body mass <100 g). We calculated the effect of tagging on apparent survival, condition, phenology and breeding performance and identified the most important predictors of the magnitude of effect sizes.

Even though the effects were not statistically significant in phylogenetically controlled models, we found a weak negative impact of geolocators on apparent survival. The negative effect on apparent survival was stronger with increasing relative load of the device and with geolocators attached using elastic harnesses. Moreover, tagging effects were stronger in smaller species.

In conclusion, we found a weak effect on apparent survival of tagged birds and managed to pinpoint key aspects and drivers of tagging effects. We provide recommendations for establishing matched control group for proper effect size assessment in future studies and outline various aspects of tagging that need further investigation. Finally, our results encourage further use of geolocators on small bird species but the ethical aspects and scientific benefits should always be considered.

Mineral resource of the month: Garnet

Released March 01, 2019 10:57 EST

2019, EARTHCARE: Global Protection of Natural Areas. (64) 98-99

Kenneth C. Curry

Garnet is the general name given to a group of complex silicate minerals, all with isometric crystal structure and similar properties and chemical composition. The most common garnet minerals are classified into three groups: the aluminum-garnet group, the chromium-garnet group and the iron-garnet group. Worldwide, garnet resources are large and occur in a wide variety of rocks, principally in metamorphic rocks such as gneisses and schists. Garnet also occurs in veins, contact metamorphic rocks, metamorphosed crystalline limestones, pegmatites and serpentinites. In addition, alluvial garnet sands are associated with heavy-mineral sand and gravel deposits in many parts of the world. 

Microclimate influences mangrove freeze damage: Implications for range expansion in response to changing macroclimate

Released March 01, 2019 10:39 EST

2019, Estuaries and Coasts

Michael J. Osland, Arik M. Hartmann, Richard H. Day, Michael S. Ross, Courtney T. Hall, Laura C. Feher, William Vervaeke

In response to warming winter air temperatures, freeze-sensitive mangrove forests are expected to expand at the expense of freeze-tolerant salt marshes. To better anticipate and prepare for mangrove range expansion, there is a need to advance understanding of the modulating role of microclimate. Here, we synthesized hypotheses regarding the effects of microclimatic variation on temperature gradients and mangrove freeze damage. Temperature data from the literature and from temperature loggers were used to quantify ecologically relevant temperature gradients. Then, literature-derived mangrove freeze damage data were used to quantify the ecological effects of these temperature gradients. Six microclimatic factors are described that produce air temperature gradients that modulate mangrove responses to winter temperature extremes: (1) distance from the ocean; (2) distance from wind buffers; (3) mangrove canopy cover; (4) height above the soil surface; (5) local slope concavity; and (6) tidal inundation. Variation in these factors produces local temperature differences that range from 2 to 14 °C, with concomitant effects on horizontal and vertical patterns of biological damage from freezing. Collectively, our results elucidate the influence of microclimate on spatial patterns of biological damage and mortality due to winter temperature extremes. As mangrove ranges expand in response to climate change, we anticipate that microclimatic variation will produce adverse environments where mangrove expansion is prohibited as well as expansion hot spots where mangroves are protected. Subsequent expansion into newly available habitat will occur from protection zones, and microclimatic gradients may even produce positive feedback cycles that ultimately accelerate the rate of range expansion in response to warming.

Hillslope hydrology in global change research and earth system modeling

Released March 01, 2019 10:35 EST

2019, Water Resources Research

Ying Fan, Martyn Clark, David M. Lawrence, Sean Swenson, L. E. Band, S. L. Brantley, P. D. Brooks, W. E. Dietrich, A. Flores, G. Grant, J. W. Kirchner, D. S. Mackay, J.J. McDonnell, Paul C. D. Milly, P. L. Sullivan, C. Tague, H. Ajami, N. W. Chaney, A. Hartmann, P. Hazenberg, J. McNamara, J. Pelletier, J. Perket, E. Rouholahnejad-Freund, T. Wagener, X. Zeng, E. Beighley, J. Buzan, M. Huang, B. Livneh, B. P. Mohanty, B. Nijssen, M. Safeeq, C. Shen, W. van Verseveld, J. Volk, D. Yamazaki

Earth System Models (ESMs) are essential tools for understanding and predicting global change, but they cannot explicitly resolve hillslope‐scale terrain structures that fundamentally organize water, energy, and biogeochemical stores and fluxes at subgrid scales. Here we bring together hydrologists, Critical Zone scientists, and ESM developers, to explore how hillslope structures may modulate ESM grid‐level water, energy, and biogeochemical fluxes. In contrast to the one‐dimensional (1‐D), 2‐ to 3‐m deep, and free‐draining soil hydrology in most ESM land models, we hypothesize that 3‐D, lateral ridge‐to‐valley flow through shallow and deep paths and insolation contrasts between sunny and shady slopes are the top two globally quantifiable organizers of water and energy (and vegetation) within an ESM grid cell. We hypothesize that these two processes are likely to impact ESM predictions where (and when) water and/or energy are limiting. We further hypothesize that, if implemented in ESM land models, these processes will increase simulated continental water storage and residence time, buffering terrestrial ecosystems against seasonal and interannual droughts. We explore efficient ways to capture these mechanisms in ESMs and identify critical knowledge gaps preventing us from scaling up hillslope to global processes. One such gap is our extremely limited knowledge of the subsurface, where water is stored (supporting vegetation) and released to stream baseflow (supporting aquatic ecosystems). We conclude with a set of organizing hypotheses and a call for global syntheses activities and model experiments to assess the impact of hillslope hydrology on global change predictions.

Prediction of ice‐free conditions for a perennially ice‐covered Antarctic lake

Released March 01, 2019 10:31 EST

2019, Journal of Geophysical Research F: Earth Surface

Maciej Obryk, P. T. Doran, J. C. Priscu

Although perennially ice‐covered Antarctic lakes have experienced variable ice thicknesses over the past several decades, future ice thickness trends and associated aquatic biological responses under projected global warming remain unknown. Heat stored in the water column in chemically stratified Antarctic lakes that have middepth temperature maxima can significantly influence the ice thickness trends via upward heat flux to the ice/water interface. We modeled the ice thickness of the west lobe of Lake Bonney, Antarctica, based on possible future climate scenarios utilizing a 1D thermodynamic model that accounts for surface radiative fluxes as well as the heat flux associated with the temperature evolution of the water column. Model results predict that the ice cover of Lake Bonney will shift from perennial to seasonal within one to four decades, a change that will drastically influence ecosystem processes within the lake.

An improved mechanical owl for efficient capture of nesting raptors

Released March 01, 2019 10:28 EST

2019, Journal of Raptor Research (53) 14-25

Meghan K. Jensen, Shanti D. Hamburg, Christopher T. Rota, David F. Brinker, Dustin L. Coles, Mark A. Manske, Vincent A. Slabe, Matthew J. Stuber, Amy B. Welsh, Todd E. Katzner

Scientific study of raptors often requires the use of a lure to capture individuals for marking or collecting various data and samples. Live lure owls in the genus Bubo are commonly used with mist nets or dho-gazas to trap nesting raptors, but the use of these live lures presents ethical, logistical, and financial challenges. Although owls mounted by taxidermists and mechanical owls have been used in place of a live bird, the success of these types of lures varies widely. We created a more realistic mechanical owl with a greater range of motion than previous models, and then tested the owl on six raptor species in a variety of habitats. For all but one species, capture rates using our mechanical owl were similar to or slightly higher than those reported in studies using live lure owls or previously designed mechanical owls. Time to capture of Northern Goshawks (Accipiter gentilis) was, on average, 8 min faster when using our mechanical owl compared to a live owl. Cost analysis revealed that both the initial expense and long-term maintenance of a mechanical owl were less than that of a live lure owl. Mechanical owls can be a useful tool for capturing raptors. Although there are some drawbacks to using a mechanical owl, our results suggest that mechanical birds are comparable to live lure owls and we believe the benefits of using a mechanical owl often outweigh the costs.

Considerations for developing wolf harvesting regulations in the contiguous United States

Released March 01, 2019 03:45 EST

2010, Journal of Wildlife Management (74) 1421-1424

L. David Mech

As gray wolves (Canis lupus) are removed from the federal Endangered Species List, management reverts to the states. Eventually most states will probably allow public wolf harvesting. Open seasons between about 1 November and 1 March accord more with basic wolf biology than during other times. Managers who consider wolf biology and public sensitivities, adapt public-taking regulations accordingly, and adjust harvest regulations as they learn will be best able to maximize the recreational value of wolf harvesting, minimize public animosity toward it, and meet their harvest objectives.

Mineral Commodity Summaries 2019

Released February 28, 2019 17:40 EST

2019, Report

Amy C. Tolcin, editor(s)

Published on an annual basis, this report is the earliest Government publication to furnish estimates covering nonfuel mineral industry data and is available at https://minerals.usgs.gov/minerals/pubs/mcs/. Data sheets contain information on the domestic industry structure, Government programs, tariffs, and 5-year salient statistics for more than 90 individual minerals and materials.

Effectiveness of lake trout (Salvelinus namaycush) suppression in Lake Pend Oreille, Idaho: 2006–2016

Released February 28, 2019 09:41 EST

2019, Hydrobiologia

Andrew M. Dux, Michael J. Hansen, Matthew P. Corsi, Nicholas C. Wahl, James P. Fredericks, Charles E. Corsi, Daniel J. Schill, Ned J. Horner

The nonnative lake trout (Salvelinus namaycush Walbaum, 1792) population in Lake Pend Oreille, Idaho increased exponentially during 1999–2006. This led to an unsustainable level of predation mortality on kokanee (Oncorhynchus nerka Walbaum, 1792), increased the conservation threat to native bull trout (Salvelinus confluentus Suckley, 1859), and jeopardized the popular recreational fishery for kokanee and rainbow trout (Oncorhynchus mykissWalbaum, 1792). In response, lake trout were suppressed since 2006 using incentivized angling, gill netting, and trap netting. From 2006 through 2016, 193,982 lake trout were removed (50% by gill netting; 44% by angling; 6% by trap netting). During this period, age-8 + (adult) lake trout abundance declined by 64%, age-3 (recruit) abundance declined by 56%, and mean total annual mortality (A) was 31.1%. Lake trout did not show evidence of a density-dependent response. Kokanee did not collapse and rebounded to abundances not observed since before lake trout expansion. Bull trout abundance declined during suppression, but the population was sustained. Lake trout suppression allowed a harvest fishery for kokanee and trophy fishery for rainbow trout to be restored. We conclude that suppression can be an effective management action for mitigating effects of nonnative lake trout in a large, deep lake.

The black brant population is declining based on mark recapture

Released February 28, 2019 09:38 EST

2019, Journal of Wildlife Management

James S. Sedinger, Thomas V. Riecke, Alan G. Leach, David H. Ward

Annual survival and recruitment in black brant (Branta bernicla nigricans) have declined since the 1990s, yet aerial surveys of the global population have been stable or even increasing over the past decade. We used a combination of a Lincoln estimator based on harvest information and band recoveries, and marked‐unmarked ratios in bag checks in 1 harvest area in Mexico to estimate the number of adults in the population during 1992–2015. We produced weighted means from the 2 kinds of estimates for years in which we had data for both, with weights equal to the inverse of the variance of the individual estimates. We treated the black brant population as consisting of 2 subpopulations. One population consisted of breeding black brant on the Yukon‐Kuskokwim Delta (YKD), Alaska, USA, and the other consisted of Arctic (northern Alaska, western Canada, and eastern Russia) breeders, and nonbreeders and failed breeders from the YKD that underwent molt migration to the Arctic. For the global population estimates, we assessed potential bias due to differential marking and harvest of the 2 subpopulations, which was approximately 1%, probably because band recovery rates were similar for the 2 subpopulations. Population estimates declined from 229,980 (average for 1999–2002) to 161,504 (average for 2012–2015). Population estimates based on estimated harvest were variable but more stable in the later years of the study, when larger numbers of brant hunters were included in the sample. We suggest that the combination of Lincoln estimates and bag check data provides a reasonable and cost effective approach to monitoring the population.

Flexible timing of annual movements across consistently used sites by Marbled Godwits breeding in Alaska

Released February 28, 2019 09:18 EST

2019, The Auk (136) 1-11

Daniel R. Ruthrauff, Lee Tibbitts, Robert E. Gill Jr.

The study of avian movement has detailed a spectrum of strategies for the timing and use of sites throughout the annual cycle, from near randomness to complete consistency. New tracking devices now permit the repeated tracking of individual animals throughout the annual cycle, detailing previously unappreciated levels of variation within migratory systems. Godwits (genus Limosa) have featured prominently in studies of avian migration, but information derived from repeated tracking of individuals is limited. The Marbled Godwit subspecies Limosa fedoa beringiae breeds on the central Alaska Peninsula, and little is known about basic aspects of its migration ecology, including the repeatability with which this population times its annual migratory movements or uses migratory and nonbreeding sites. To address these questions, we equipped 9 Marbled Godwits breeding at a site near Ugashik, Alaska, with solar-powered satellite transmitters. We tracked individuals from July, 2008 to October, 2015 and obtained repeat migratory tracks from 5 of these birds. Individuals exhibited high fidelity to breeding, nonbreeding, and migratory stopover sites across years, but in contrast to congeners that conduct consistently timed, long, nonstop migrations, beringiaeMarbled Godwits exhibited low levels of individual- or population-level repeatability in the timing of migratory movements. Their relatively short migrations may enable the integration of local environmental cues, potentially facilitating individual flexibility in the timing of annual migratory movements. Curiously, if local cues ultimately drive the timing of Marbled Godwit migratory movements, the population’s relatively constrained distribution during both the breeding and nonbreeding season should serve to synchronize birds if they are responding to similar cues. That our sample of Marbled Godwits nonetheless exhibited within- and between-year variation in the timing of their migratory movements suggests a complex integration of annually variable internal and external cues.

A multidisciplinary framework to derive global river reach classifications at high spatial resolution

Released February 27, 2019 16:29 EST

2019, Environmental Research Letters (14) 1-12

Camille Ouellet Dallaire, Bernhard Lehner, Roger Sayre, Michele Thieme

Projected climate and environmental change are expected to increase the pressure on global freshwater resources. To prepare for and cope with the related risks, stakeholders need to devise plans for sustainable management of river systems, which in turn requires the identification of management-appropriate operational units, such as groups of rivers that share similar environmental and biological characteristics. Ideally, these units are of a manageable size, and are biotically or abiotically distinguishable across a variety of river types. Here, we aim to address this need by presenting a new global river classification framework (GloRiC) to establish a common vocabulary and standardized approach to the development of globally comprehensive and integrated river classifications that can be tailored to different goals and requirements. We define the GloRiC conceptual framework based on five categories of variables: (1) hydrology; (2) physiography and climate; (3) fluvial geomorphology; (4) water chemistry; and (5) aquatic biology. We then apply the framework using hydro-environmental attributes provided by a seamless high-resolution river reach database to create initial instances of three sub-classifications (hydrologic, physio-climatic, and geomorphic) which we ultimately combine into 127 river reach types at the global scale. These supervised classifications utilize a mix of statistical analyses and expert interpretation to identify the classifier variables, the number of classes, and their thresholds. In addition, we also present an unsupervised, multivariable k-means statistical clustering of all river reaches into 30 groups. These first-of-their-kind global river reach classifications at high spatial resolution provide baseline information for a total of 35.9 million kilometers of rivers that have been assessed in this study, and are expected to be particularly useful in remote or data-poor river basins. The GloRiC framework and associated data are primarily designed for broad and rapid applicability in assessments that require stratified analyses of river ecosystem conditions at global and regional scales; smaller-scale applications could follow the same conceptual framework yet use more detailed data sources.

A new 30 meter resolution global shoreline vector and associated global islands database for the development of standardized ecological coastal units

Released February 27, 2019 15:48 EST

2019, Journal of Operational Oceanography

Roger Sayre, Suzanne Noble, Sharon L. Hamann, Rebecca Smith, Dawn J. Wright, Sean P. Breyer, Kevin Butler, Keith Van Graafeiland, Charlie Frye, Deniz Karagulle, Dabney Hopkins, Drew Stephens, Kevin Kelly, Zeenatul Basher, Devon Burton, Jill Janene Cress, Karina Atkins, D. Paco Van Sistine, Beverly Friesen, Rebecca Allee, Tom Allen, Peter Aniello, Irawan Asaad, Mark John Costello, Kathy Goodin, Peter Harrison, Maria T. Kavanaugh, Helen Lillis, Eleonora Manca, Frank E. Muller-Karger, Bjorn Nyberg, Rost Parsons, Justin Saarinen, Jac Steiner, Adam Reed

A new 30-m spatial resolution global shoreline vector (GSV) was developed from annual composites of 2014 Landsat satellite imagery. The semi-automated classification of the imagery was accomplished by manual selection of training points representing water and non-water classes along the entire global coastline. Polygon topology was applied to the GSV, resulting in a new characterisation of the number and size of global islands. Three size classes of islands were mapped: continental mainlands (5), islands greater than 1 km2 (21,818), and islands smaller than 1 km2 (318,868). The GSV represents the shore zone land and water interface boundary, and is a spatially explicit ecological domain separator between terrestrial and marine environments. The development and characteristics of the GSV are presented herein. An approach is also proposed for delineating standardised, high spatial resolution global ecological coastal units (ECUs). For this coastal ecosystem mapping effort, the GSV will be used to separate the nearshore coastal waters from the onshore coastal lands. The work to produce the GSV and the ECUs is commissioned by the Group on Earth Observations (GEO), and is associated with several GEO initiatives including GEO Ecosystems, GEO Marine Biodiversity Observation Network (MBON) and GEO Blue Planet.

Adapting a regional water-quality model for local application: A case study for Tennessee, USA

Released February 27, 2019 12:59 EST

2019, Environmental Modelling and Software (115) 187-199

Anne B. Hoos, Sherry H. Wang, Gregory E. Schwarz

We evaluated whether SPAtially Referenced Regression On Watershed attributes (SPARROW) models calibrated for two adjacent USA regions could be applied at the local scale to support management decisions for streams in Tennessee. Nutrient-source apportionment of load is important for this local-scale application and demands careful consideration of uncertainty in the calibrated coefficients. We used Gauss-Newton regression to test the published SPARROW models for constancy of coefficient estimates between calibration sites on streams within (n = 59) versus outside (n = 327) Tennessee and concluded source apportionment was unbiased for Tennessee streams. The SPARROW models were then applied without re-calibration to predict stream loads and source apportionment for Tennessee streams and to build tools for displaying model results and evaluating source-change scenarios. This approach may inform the adaptation of other regional-scale regression models for use to address water-resource management issues in smaller-scale watersheds.

Geochemically distinct oil families in the onshore and offshore Santa Maria basins, California

Released February 27, 2019 12:56 EST

2019, AAPG Bulletin (103) 243-271

Kenneth E. Peters, Paul G. Lillis, Thomas Lorenson, J. E. Zumberge

The purpose of this work is to identify genetic affinities among 48 crude oil samples from the onshore and offshore Santa Maria basins. A total of 21 source-related biomarker and stable carbon isotope ratios among the samples were assessed to assure that they were unaffected by secondary processes. Chemometric analysis of these data identifies six oil families with map and stratigraphic distributions that reflect organofacies variations within the Miocene Monterey Formation source rock. The data comprise a training set that was used to create a chemometric decision tree to classify newly collected oil samples. Three onshore families originated from two synclines, which may contain one or more pods of thermally mature source rock. Multiple biomarker parameters indicate that the six oil families achieved early oil window maturity in the range of 0.6%–0.7% equivalent vitrinite reflectance. The offshore oil samples consist of one family from Point Pedernales field and two families from the “B” prospect. Geochemical characteristics of these families indicate origins under differing water column and sediment oxicity and carbonate versus siliceous and detrital input in ‘carbonate,’ ‘marl,’ and ‘shale’ organofacies like those in the lower calcareous–siliceous, carbonaceous marl, and clayey–siliceous members of the Monterey Formation elsewhere in coastal California. The corresponding lithofacies and organofacies appear to be linked to the early–middle Miocene climate optimum and subsequent paleoclimatic cooling after circa 14 Ma, a systematic up-section increase in the stable carbon isotope composition of related oil samples, decreased preservation of calcium carbonate shells from planktic foraminifera and coccoliths, and increased preservation of clay-sized siliceous shells of diatoms and radiolarians. The results show that organofacies within the Monterey source rock are responsible for many of the geochemical differences between the oil families. This paleoclimate–organofacies model for crude oil from the Monterey Formation can be used to enhance future exploration efforts in many areas of coastal California.

Adaptive variation, including local adaptation, requires decades to become evident in common gardens

Released February 27, 2019 12:53 EST

2019, Ecological Applications (29) 1-7

Matthew J. Germino, Ann M. Moer, Alan R. Sands

Population‐level adaptation to spatial variation in factors such as climate and soils is critical for climate‐vulnerability assessments, restoration seeding, and other ecological applications in species management, and the underlying information is typically based on common‐garden studies that are short duration. Here, we show >20 yr were required for adaptive differences to emerge among 13 populations of a widespread shrub (sagebrush, Artemisia tridentata ssp wyomingensis) collected from around the western United States and planted into common gardens. Additionally, >10 yr were required for greater survival of local populations, that is, local adaptation, to become evident. Variation in survival was best explained by the combination of populations’ home ecoregion combined with grouping of minimum temperature and aridity. Additional reductions in survival were explained by ungrouped (i.e., continuous) measures of garden‐to‐population‐origin separation in geographic distance (5% decrease in survival per 100 km increase in separation; R2 = 0.22) and especially in minimum temperature in younger plants (−4% per + °C difference, R2 = 0.56 vs. 0.29 in the 14th vs. 27th post‐planting years, respectively). Longer‐term common garden studies are needed. While we await them, uncertainty in adaptive variation resulting from short‐term observations could be quantitatively estimated and reported with seed‐transfer guidelines to reduce risks of introducing maladapted provenances in restoration.

Bridge scour countermeasure assessments at select bridges in the United States, 2016–18

Released February 27, 2019 07:11 EST

2019, Open-File Report 2019-1008

Taylor J. Dudunake, Richard J. Huizinga, Ryan L. Fosness

In 2009, the Federal Highway Administration published Hydraulic Engineering Circular No. 23 (HEC-23) to provide specific design and implementation guidelines for bridge scour and stream instability countermeasures. However, the effectiveness of countermeasures implemented over the past decade following those guidelines has not been evaluated. Therefore, in 2013, the U.S. Geological Survey, in cooperation with the Federal Highway Administration, began a study to assess the current condition of bridge-scour countermeasures at selected sites to evaluate their effectiveness. Bridge-scour countermeasures were assessed during 2016–2018 after additional sites were added following a similar study. Site assessments included reviewing countermeasure design plans, summarizing the peak and daily streamflow history, and assessments at each site. Each site survey included a photo log summary, field form, and topographic and bathymetric geospatial data and metadata. This report documents the study area and site-selection criteria, explains the survey methods used to evaluate the condition of countermeasures, and presents the complete documentation for each countermeasure assessment.

Planetary geologic mapping—Program status and future needs

Released February 27, 2019 07:01 EST

2019, Open-File Report 2019-1012

James A. Skinner Jr., Alexandra E. Huff, Corey M. Fortezzo, Tenielle Gaither, Trent M. Hare, Marc A. Hunter, Holly Buban

The United States Geological Survey’s (USGS) Planetary Geologic Map Coordination Group (Flagstaff, Ariz.) surveyed planetary geoscience map makers and users to determine the importance, relevance, and usability of such products to their planetary science research and to current and future needs of the planetary science community. This survey was prepared because the planetary science community lacks a modern assessment of the value invested in geoscience map products and processes (including the diverse scientific and technical personnel who add to and maintain this infrastructure) and a strategy that ensures these efforts appropriately prioritize mapping efforts across all solid surface bodies in the Solar System.

A 30-question survey was conducted through an online questionnaire and was designed to (1) take <10 minutes, (2) instill a sense that responses would be acted upon, and (3) encourage community participation through a user-friendly interface. The survey made a distinction between “standardized” geoscience maps (those published by the USGS that require adherence to specific cartographic standards, conventions, and principles) and “non-standardized” geoscience maps (those published by other venues such as peer-reviewed journals that are not required to, but might, adhere to some cartographic standards, conventions, and principles). The survey was opened on Sunday, March 18, 2017 (to coincide with the annual Lunar and Planetary Science Conference in The Woodlands, Tex.) and was closed on Thursday, May 25, 2017. There was a total of 265 unique responses that were formulated into 17 unique findings that were matched with one or more recommendations to be addressed by the planetary science community.

Long-term nitrogen addition shifts the soil nematode community to bacterivore-dominated and reduces its ecological maturity in a subalpine forest

Released February 26, 2019 15:03 EST

2019, Soil Biology and Biochemistry (130) 177-184

E. Ashley Shaw, Claudia M. Boot, John C. Moore, Diana H. Wall, Jill S. Baron

Nitrogen deposition from anthropogenic sources is a global problem that reaches even the most remote ecosystems. Responses belowground vary by ecosystem, and have feedbacks to geochemical processes, including carbon storage. A long-term nitrogen addition study in a subalpine forest has shown carbon loss over time, atypical for a forest ecosystem. Loss of microbial biomass is likely linked to lower soil carbon, but the mechanism behind this is still unknown. One possible explanation is through increased turnover due to grazing by soil fauna. Because nematodes occupy many trophic levels and are sensitive to trophic and environmental changes, assessing their communities helps reveal belowground responses. In this study, we tested the hypothesis that long-term nitrogen fertilization affects nematode community structure and maturity beneath coniferous forests in the Rocky Mountains, indicating a faster cycling, bacterial-driven system. We identified and enumerated nematodes by trophic group and family from experimental plots. Total nematode abundance was 40–96% greater in fertilized plots compared to the control, but richness, diversity, and ecological maturity were lower. The differences in abundance were driven by opportunistic bacterivores (e.g., Rhabditidae) and plant parasites (e.g., Tylenchidae), which made up 23 and 13% of the community in fertilized compared to 7 and 5% in control plots, respectively. Nematode maturity indices showed that the nematode food webwas enriched (indicating high nutrient/resource status) and structured (all trophic levels present, including long-lived predators) in both treatments, but significantly more enriched in the fertilized treatment. Nonmetric multidimensional scaling of the relative abundance of nematode families demonstrated that nematode community composition differed between treatments, driven largely by opportunistic bacterivores (e.g., Rhabditidae) in the fertilized plots. The mechanism of the aboveground–belowground link between nitrogen deposition and nematode community composition is likely through increased microbial turnover, and sustained high-quality food for microbial grazing nematodes.

Applying concepts of general resilience to large river ecosystems: A case study from the Upper Mississippi and Illinois rivers

Released February 26, 2019 15:01 EST

2019, Ecological Indicators (101) 1094-1110

Kristen L. Bouska, Jeffrey N. Houser, Nathan R. De Jager, Molly Van Appledorn, James T. Rogala

Large floodplain-river ecosystems are often highly modified to provide services that society desires, yet these modifications can limit an ecosystem’s ability to adapt to changing conditions. The adaptive capacity of an ecosystem, its general resilience, is a conceptual framework for considering how a system will respond to such changes. We sought to apply aspects of three general resilience principles (diversity and redundancy, connectivity, and controlling variables) to our understanding of floodplain-river ecosystem structure and function. We demonstrate the applicability of this approach in a case study of the Upper Mississippi River System (UMRS). In doing so, we developed ten indicators that highlight important structural and functional aspects of this floodplain-river ecosystem, and likely underlie the capacity of large rivers to cope with environmental change and disturbance. We developed diversity and redundancy indicators for aquatic habitats, patterns of floodplain inundation, and fish communities. Connectivity indicators included metrics of longitudinal and lateral connections. Controlling variable indicators included deviations from historic water surface elevation fluctuations, water clarity, nutrient concentrations, and aquatic invasive species. This set of indicators provides a simple description of the adaptive capacity of four distinct reaches of the UMRS: Upper Impounded, Lower Impounded, Unimpounded Reaches of the Upper Mississippi River and the entire Illinois River. High aquatic habitat diversity and redundancy, fish functional diversity and redundancy, and water clarity, and the scarcity of invasive fish species are all factors that likely contribute to the high general resilience of the Upper Impounded Reach. However, the limited longitudinal connectivity and establishment of a minimum water level for navigation are factors that may inhibit the general resilience of this reach. In the Lower Impounded Reach, there is high within-reach variability for individual indicators such as aquatic habitat diversity, fish functional diversity and redundancy, and longitudinal and lateral connectivity. In the Unimpounded Reach, a high degree of longitudinal connectivity likely enhances its general resilience, but low aquatic habitat diversity, low lateral connectivity, and relatively high number of invasive fish species inhibit general resilience. For the Illinois River Reach, the relatively high fish functional diversity and redundancy likely contributes to its general resilience, whereas high number of invasive fish species, low water clarity, low lateral connectivity, and high range of water levels may inhibit general resilience. Indicators derived from application of concepts of general resilience provide insight into the current coping capacity of the UMRS and identify opportunities for enhancing resilience.

Escherichia coli and microbial source tracking marker concentrations in and near a constructed wetland in Maumee Bay State Park, Oregon, Ohio, 2015–16

Released February 26, 2019 14:45 EST

2019, Scientific Investigations Report 2018-5127

Christopher M. Kephart, Amie M.G. Brady, Ryan W. Jackwood

Elevated Escherichia coli (E. coli) concentrations at the Maumee Bay State Park (MBSP) Lake Erie beach have resulted in frequent recreational water-quality advisories. After the construction of a wetland along Berger Ditch in Maumee Bay State Park, Oregon, Ohio, samples were collected and analyzed for concentrations of E. coli and microbial source tracking (MST) markers. This study was done by the U.S. Geological Survey, in cooperation with the University of Toledo, to provide data that can be used to help evaluate the effects of the wetland on water quality in MBSP. From July 2015 to February 2016, 116 samples were collected from six sites. Median GenBac (general marker) and E. coli concentrations were higher in samples from Berger Ditch sites than in samples from the wetland sites. No statistically significant difference was found between median E. coli concentrations in samples collected at Berger Ditch sites upstream and downstream from the wetland. The frequency of detection of the human-associated Bacteroides MST marker (HF183) decreased from 39 percent upstream from the wetland to 22 percent downstream from the wetland; however, the HF183 median concentrations from these two groups of samples were nearly the same (2,700 to 2,800 copies per 100 milliliters from upstream to downstream). The waterfowl-associated Helicobacter MST marker (GFD) was detected in 13 percent of samples from the Berger Ditch site upstream from the wetland, although it was not detected in samples from the Berger Ditch site downstream from the wetland. The ruminant-associated MST marker, Rum2Bac, was not detected at any site during this study.

Effects of life history and reproduction on recruitment time lags in reintroductions of rare plants

Released February 26, 2019 14:29 EST

2019, Conservation Biology

Matthew A. Albrecht, Oyomoare L. Osazuwa-Peters, Joyce Maschinski, Timothy J. Bell, Marlin L. Bowles, William E. Brumback, Janice Duquesnel, Michael Kunz, Jimmy Lange, Kimberlie A. McCue, A. Kathryn McEachern, Sheila Murray, Peggy Olwell, Noel B. Pavlovic, Cheryl L. Peterson, Jennifer Possley, John L. Randall, Samuel J. Wright

Reintroductions are important components of conservation and recovery programs for rare plant species, but their long‐term success rates are poorly understood. Previous reviews of plant reintroductions focused on short‐term (e.g., ≤3 years) survival and flowering of founder individuals rather than on benchmarks of intergenerational persistence, such as seedling recruitment. However, short‐term metrics may obscure outcomes because the unique demographic properties of reintroductions, including small size and unstable stage structure, could create lags in population growth. We used time‐to‐event analysis on a database of unusually well‐monitored and long‐term (4–28 years) reintroductions of 27 rare plant species to test whether life‐history traits and population characteristics of reintroductions create time‐lagged responses in seedling recruitment (i.e., recruitment time lags [RTLs]), an important benchmark of success and indicator of persistence in reintroduced populations. Recruitment time lags were highly variable among reintroductions, ranging from <1 to 17 years after installation. Recruitment patterns matched predictions from life‐history theory with short‐lived species (fast species) exhibiting consistently shorter and less variable RTLs than long‐lived species (slow species). Long RTLs occurred in long‐lived herbs, especially in grasslands, whereas short RTLs occurred in short‐lived subtropical woody plants and annual herbs. Across plant life histories, as reproductive adult abundance increased, RTLs decreased. Highly variable RTLs were observed in species with multiple reintroduction events, suggesting local processes are just as important as life‐history strategy in determining reintroduction outcomes. Time lags in restoration outcomes highlight the need to scale success benchmarks in reintroduction monitoring programs with plant life‐history strategies and the unique demographic properties of restored populations. Drawing conclusions on the long‐term success of plant reintroduction programs is premature given that demographic processes in species with slow life‐histories take decades to unfold.

Landsat: The cornerstone of global land imaging

Released February 26, 2019 14:23 EST

2019, GIM International (January/February 2019) 31-35

Ginger Butcher, Christopher Barnes, Linda Owen

Since 1972, the joint NASA/ U.S. Geological Survey Landsat series of Earth Observation satellites have provided an uninterrupted space-based data record of the Earth’s land surface to help advance scientific research towards the understanding of our planet and the environmental impact of its inhabitants. Early Landsat satellites offered a wealth of new data that improved mapping of remote areas and geologic features along with digital analysis of vegetation. The utility of Landsat’s spatial and spectral resolution has advanced its use for applications that benefit society such as global crop forecasting, forest monitoring, water use, carbon assessments, and the base for Google Maps. Landsat’s long-term data record provides an unrivaled resource for observing land cover and land-use change over a timescale of decades. The free and open Landsat data policy in 2008 was a paradigm shift for the world. Today, due to improved analytical and computing capabilities, the Landsat archive is poised to shift into a more real-time monitoring and understanding of the Earth.

Diurnal habitat selection of migrating Whooping Crane in the Great Plains

Released February 26, 2019 14:19 EST

2019, Avian Conservation and Ecology (14) 1-14

David M. Baasch, Patrick D. Farrell, Aaron T. Pearse, David A. Brandt, Andrew J. Caven, Mary J. Harner, Greg D. Wright, Kristine L. Metzger

Available stopover habitats with quality foraging opportunities are essential for migrating waterbirds, including Whooping Crane (Grus americana). Several studies have evaluated habitats used by Whooping Crane for roosting throughout its migration corridor; however, habitats associated with foraging and other diurnal activities have received less attention. We used data collected from 42 Whooping Crane individuals that included 2169 diurnal use locations within 395 stopover sites evaluated during spring 2013 to fall 2015 to assess diurnal habitat selection throughout the U.S. portion of the migration corridor. We found that Whooping Crane selected wetland land-cover types (i.e., open water, riverine, and semipermanent wetlands) and lowland grasslands for diurnal activities over all other land-cover types that we evaluated, including croplands. Whooping Crane generally avoided roads, and avoidance varied based on land-cover class. There has been considerable alteration and destruction of natural wetlands and rivers that serve as roosting and foraging sites for migrating Whooping Crane. Given recent droughts and the likelihood of future landscape changes within the migration corridor, directing conservation efforts toward protecting and enhancing wetland stopover areas may prove critical for continued growth of the last remaining wild population of Whooping Crane. Future studies of this Whooping Crane population should focus on specific wetland complexes and riverine sites throughout the migration corridor to identify precise management actions that could be taken to enhance and protect these imperilled land-cover types.

Linking fire and the United Nations Sustainable Development Goals

Released February 26, 2019 14:16 EST

2019, Science of the Total Environment (662) 547-558

Deborah A. Martin

Fire is a ubiquitous natural disturbance that affects 3–4% of the Earth's surface each year. It is a tool used by humans for land clearing and burning of agricultural wastes. The United Nations Sustainable Development Goals (SDGs) do not explicitly mention fire, though many of the Goals are affected by the beneficial and adverse consequences of fires on ecosystem services. There are at least three compelling reasons to include a fire perspective in the implementation of the United Nations Sustainable Development Goals. The first reason relates to the stated vision of the United Nations 2030 Agenda to protect the environment. In order to achieve environmental protection during sustainable development activities, it is necessary to understand and plan for the effects of disturbances, in this case fire, on ecosystem services. The second reason is that fires produce emissions with regional and global impacts on air quality and rainfall patterns. Fires contribute to global warming though the release greenhouse gases, primarily CO2, and black carbon, identified as a SLCP (short-lived climate pollutant). The third reason is that fire is one of several complex processes that lead to land degradation across the globe. Opportunities exist to incorporate a fire perspective into sustainable development projects or approaches. Two examples are highlighted here. Transdisciplinary communication and collaboration are needed to address the complex issues related to fire, and to climate and land use change.

Disease‐structured N‐mixture models: A practical guide to model disease dynamics using count data

Released February 26, 2019 14:14 EST

2019, Ecology and Evolution (9) 899-909

Graziella V. DiRenzo, Christian Che-Castaldo, Sarah P. Saunders, Evan H. Campbell Grant, Elise F. Zipkin

Obtaining inferences on disease dynamics (e.g., host population size, pathogen prevalence, transmission rate, host survival probability) typically requires marking and tracking individuals over time. While multistate mark–recapture models can produce high‐quality inference, these techniques are difficult to employ at large spatial and long temporal scales or in small remnant host populations decimated by virulent pathogens, where low recapture rates may preclude the use of mark–recapture techniques. Recently developed N‐mixture models offer a statistical framework for estimating wildlife disease dynamics from count data. N‐mixture models are a type of state‐space model in which observation error is attributed to failing to detect some individuals when they are present (i.e., false negatives). The analysis approach uses repeated surveys of sites over a period of population closure to estimate detection probability. We review the challenges of modeling disease dynamics and describe how N‐mixture models can be used to estimate common metrics, including pathogen prevalence, transmission, and recovery rates while accounting for imperfect host and pathogen detection. We also offer a perspective on future research directions at the intersection of quantitative and disease ecology, including the estimation of false positives in pathogen presence, spatially explicit disease‐structured N‐mixture models, and the integration of other data types with count data to inform disease dynamics. Managers rely on accurate and precise estimates of disease dynamics to develop strategies to mitigate pathogen impacts on host populations. At a time when pathogens pose one of the greatest threats to biodiversity, statistical methods that lead to robust inferences on host populations are critically needed for rapid, rather than incremental, assessments of the impacts of emerging infectious diseases.

Catchment-level estimates of nitrogen and phosphorus agricultural use from commercial fertilizer sales for the conterminous United States, 2012

Released February 26, 2019 12:06 EST

2019, Scientific Investigations Report 2018-5145

Jana S. Stewart, Gregory E. Schwarz, John W. Brakebill, Stephen D. Preston

Nutrient inputs from commercial agricultural fertilizer, particularly nitrogen and phosphorus, are important factors contributing to the degradation of surface-water quality and the alteration of aquatic ecosystems. Despite this importance, information about the application of fertilizer to agricultural land is not available in a consistent manner across the United States at a scale useful for regional water-quality assessment. To address this need, an approach is developed to relate commercial fertilizer sales to a set of explanatory variables using spatially referenced modeling methods. Spatially referenced modeling in this study refers to statistically relating fertilizer use, estimated from commercial fertilizer sales data, to spatially referenced data on watershed attributes. Separate models for nitrogen and phosphorus are developed to estimate elemental fertilizer use on agricultural lands for the conterminous United States at the National Hydrography Dataset Plus (NHDPlus) catchment scale for the year 2012. The approach builds on earlier efforts that use Association of American Plant Food Control Officials data on fertilizer sales to provide county-level estimates of nitrogen and phosphorus fertilizer use. The spatially referenced method improves on these efforts by allowing for varying nitrogen to phosphorus ratios at the catchment scale and expanding the set of variables used to allocate county-level sales data to the catchment scale. The models include catchment-level factors that are either primary determinants of fertilizer use, such as the acreage of different crop types, or measures reflecting the intensity of use, such as climate. Explanatory variables available only at the county scale, such as U.S. Department of Agriculture Census of Agriculture estimates of fertilizer expenditures, are included to improve the model predictions of elemental use. The nitrogen and phosphorus models explain more than 90 percent of the variation in elemental use at the state level, and the statistical approach allows for the estimation of uncertainty of predicted use in each catchment. The spatial patterns of model predictions reflect known agricultural cropping practices across the United States that transcend political boundaries, despite the county/state orientation of the fertilizer sales information. The results are expected to be useful for a variety of water-quality assessments that are intended to estimate nitrogen and phosphorus loads to streams.

Shallow geology, sea-floor texture, and physiographic zones of the inner continental shelf from Aquinnah to Wasque Point, Martha’s Vineyard, and Eel Point to Great Point, Nantucket, Massachusetts

Released February 26, 2019 11:45 EST

2019, Open-File Report 2018-1181

Elizabeth A. Pendleton, Wayne E. Baldwin, Seth D. Ackerman, David S. Foster, Brian D. Andrews, William C. Schwab, Laura L. Brothers

A series of interpretive maps that describe the shallow geology, distribution, and texture of sea-floor sediments, and physiographic zones of the sea floor along the south and west shores of Martha’s Vineyard and the north shore of Nantucket, Massachusetts, were produced by using high-resolution geophysical data (interferometric and multibeam swath bathymetry, light detection and ranging (lidar) bathymetry, backscatter intensity, and seismic-reflection profiles), sediment samples, and bottom photographs. These interpretations are intended to aid statewide efforts to inventory and manage coastal and marine resources, link with existing data interpretations, and provide information for research focused on coastal evolution and environmental change. Marine geologic mapping of the inner continental shelf of Massachusetts is a statewide cooperative effort of the U.S. Geological Survey and the Massachusetts Office of Coastal Zone Management.

Spatial distribution of band recoveries of black brant

Released February 25, 2019 13:51 EST

2019, Journal of Wildlife Management (83) 304-311

Alan G. Leach, David H. Ward, James S. Sedinger, Thomas V. Riecke, Jerry W. Hupp, Robert J. Ritchie

On average, band recovery rates of adult black brant (Branta bernicla nigricans) more than doubled between the 2000s and 2010s. However, the spatial distribution of band recoveries of black brant has not been reported. Our objective was to describe the spatial distribution of band recoveries of black brant since 1990. We found that Alaska, California, and Mexico accounted for ≥89% of band recoveries for black brant released from the Arctic and the Tutakoke River Colony in southwestern Alaska, in each decade studied. Although recovery rates increased in each major harvest region from the 1990s to 2010s, increases were not even. For brant released from the Arctic, the recovery rate in Alaska has gone up 7‐fold, whereas the recovery rate in Mexico has increased 1.3‐fold since the 1990s. For brant banded in the Arctic, the increased recovery rates in Alaska resulted largely from a rise in recoveries from the Izembek Lagoon area. For brant banded at the Tutakoke River Colony, the recovery rate in Alaska increased 4.8‐fold, whereas recovery rates in Mexico increased 1.6‐fold. Despite the reduced relative contribution of Mexico to band recoveries in the 2010s, Bahia San Quintin, Mexico, still contributes more recoveries than any other wintering estuary. Because 57–60% of black brant band recoveries occur at the localities of Izembek Lagoon, Alaska; Humboldt Bay, California; and Bahia San Quintin, it is likely that accurate annual estimates of the black brant population using Lincoln's method could be derived from hunter bag checks at these 3 areas. If population managers are interested in managing harvest rates of black brant, they could focus efforts on the main hunting areas we highlight in this paper. Finally, it is unclear if the recent increases in band recovery rates are the result of increased harvest, a declining population, or both; therefore, we suggest refinement of population monitoring programs and continued monitoring of band recovery rates.

Modeling riparian restoration impacts on the hydrologic cycle at the Babacomari Ranch, SE Arizona, USA

Released February 25, 2019 13:49 EST

2019, Water (11) 1-20

Laura M. Norman, James B. Callegary, Laurel Lacher, Natalie R. Wilson, Chloé Fandel, Brandon T. Forbes, Tyson Swetnam

This paper describes coupling field experiments with surface and groundwater modeling to investigate rangelands of SE Arizona, USA using erosion-control structures to augment shallow and deep aquifer recharge. We collected field data to describe the physical and hydrological properties before and after gabions (caged riprap) were installed in an ephemeral channel. The modular finite-difference flow model is applied to simulate the amount of increase needed to raise groundwater levels. We used the average increase in infiltration measured in the field and projected on site, assuming all infiltration becomes recharge, to estimate how many gabions would be needed to increase recharge in the larger watershed. A watershed model was then applied and calibrated with discharge and 3D terrain measurements, to simulate flow volumes. Findings were coupled to extrapolate simulations and quantify long-term impacts of riparian restoration. Projected scenarios demonstrate how erosion-control structures could impact all components of the annual water budget. Results support the potential of watershed-wide gabion installation to increase total aquifer recharge, with models portraying increased subsurface connectivity and accentuated lateral flow contributions.

Optimizing historic preservation under climate change: Decision support for cultural resource adaptation planning in national parks

Released February 25, 2019 13:44 EST

2019, Land Use Policy (83) 379-389

Xiao Xiao, Erin Seekamp, Max Post van der Burg, Mitchell Eaton, Sandra Fatorić, Allie McCreary

Climate change poses great challenges for cultural resource management, particularly in coastal areas. Cultural resources, such as historic buildings, in coastal areas are vulnerable to climate impacts including inundation, deterioration, and destruction from sea-level rise and storm-related flooding and erosion. However, research that assesses the trade-offs between actions for protecting vulnerable and valuable cultural resources under budgetary constraints is limited. This study focused on developing a decision support model for managing historic buildings at Cape Lookout National Seashore. We designed the Optimal Preservation Decision Support (OptiPres) model to: (a) identify optimal, annual adaptation actions for historic buildings across a 30-year planning horizon, (b) quantify trade-offs between different actions and the timing of adaptation actions under constrained budgets, and (c) estimate the effectiveness of budget allocations on the resource value of historic buildings. Our analysis of the model suggests that: (1) funding allocation thresholds may exist for national parks to maintain the historical significance and use potential of historic buildings under climate change, (2) the quantitative assessment of trade-offs among alternative adaptation actions provides generalizable guidance for decision makers about the dynamics of their managed system, and (3) the OptiPres model can identify cost-efficient approaches to allocate funding to maintain the historical value of buildings vulnerable to the effects of climate change. Therefore, the OptiPres model, while not designed as a prescriptive decision tool, allows managers to understand the consequences of proposed adaptation actions. The OptiPres model can guide park managers to make cost-effective climate adaptation decisions for historic buildings more transparently and robustly.

Modeling δ18O as an early indicator of regime shift arising from salinity stress in coastal vegetation

Released February 25, 2019 13:41 EST

2019, Hydrogeology Journal

Su Yean Teh, Hock Lye Koh, Donald L. DeAngelis, Clifford I. Voss, Leonel da Silveira Lobo Sternberg

In many important coastal habitats, a combination of increasing soil salinization due to sea level rise, reduced precipitation and storm surges may induce regime shift from salinity-intolerant glycophytic vegetation to salinity-tolerant halophytic species. Early detection of regime shift due to salinity stress in vegetation may facilitate conservation efforts. It has been shown that the 18O value of water in the xylem of trees can be used as a surrogate for salinity in the rooting zone of plants. Coupling measured δ18O values in the tree xylem with simulated δ18O values in trees and salinity in the vadose zone can be used to investigate competitive responses of glycophytic versus halophytic trees. MANTRA-O18 simulations suggest that the impacts of salinization on diminishing the resilience of salinity-intolerant trees can be detected up to 25 years before the glycophytic trees are threatened with regime shift to halophytic species. This early detection provides critical lead time and valuable information and insights useful for planning adaptation strategy to mitigate against the adverse impacts of sea level rise and climate change.

The Earth Mapping Resources Initiative (Earth MRI): Mapping the nation’s critical mineral resources

Released February 25, 2019 11:15 EST

2019, Fact Sheet 2019-3007

Warren C. Day

The Earth Mapping Resources Initiative (Earth MRI; formerly known as 3DEEP) is planned as a partnership between the U.S. Geological Survey (USGS), the Association of American State Geologists (AASG), and other Federal, State, and private-sector organizations. The goal of the effort is to improve our knowledge of the geologic framework in the United States and to identify areas that have the potential to contain undiscovered critical mineral resources. Enhancement of our domestic mineral supply will decrease our reliance on foreign sources of minerals that are fundamental to the Nation’s security and economy.

The intent of Earth MRI is to leverage the USGS’s existing relationships with States and the private sector to conduct state-of-the-art geologic mapping and airborne geophysical and topographic (lidar) surveys. Analyses of these datasets could point to potential buried critical mineral deposits.

Coagulant and sorbent efficacy in removing mercury from surface waters in the Cache Creek watershed, California

Released February 25, 2019 10:44 EST

2019, Open-File Report 2019-1001

Erica R. De Parsia, Jacob A. Fleck, David P. Krabbenhoft, Kim Hoang, David Roth, Paul Randall

Cache Creek drains part of northern California’s Coast Ranges and is an important source of mercury (Hg) to the Sacramento–San Joaquin Delta. Cache Creek is contaminated with Hg from several sources, including historical Hg and gold mines, native Hg in the soils, and active mineral springs. In laboratory experiments in a study conducted by the U.S. Geological Survey, in cooperation with the U.S. Environmental Protection Agency, the use of coagulants and sorbents to immobilize Hg in water samples from high-concentration sources in the Cache Creek watershed was investigated. Three sites were selected for the collection of surface-water samples containing high and low concentrations of particulate-associated Hg. The high-particulate Hg samples were collected from Cache Creek Settling Basin during stormflow conditions. The low-particulate Hg samples were collected from two geochemically contrasting sites during base-flow conditions (downstream from a geothermal spring and at the emergence point of a connate-water spring). Three coagulants were chosen for laboratory testing with the high-particulate sample— (1) ChitoVanTM HV 1.5 percent (shell based), (2) FerralyteTM 8131 (ferric sulfate based), and (3) UltrionTM 8186 (aluminum based). Each coagulant was tested at various dose amounts to determine the optimum dose rate for the high-particulate sample. The low-particulate source samples were passed through three sorbents—(1) chitosan flakes, (2) coconut shell-based activated carbon, and (3) coal-based activated carbon. In-line columns were packed with each material, and the untreated sample was passed through each column at three different flow rates (0.1, 0.5, and 1.0 liter per minute, L/min).

For dose rates used in this study, ChitoVanTM reduced turbidity of the particulate sample by 85–91 percent, FerralyteTM reduced turbidity by 54–93 percent, and UltrionTM reduced turbidity by greater than 90 percent. At the lowest dose rate, ChitoVanTM achieved a 59- to 61-percent reduction in whole-water methylmercury (MeHg) concentrations and a 71- to 75-percent decrease in whole-water total mercury (THg) concentrations. FerralyteTM achieved a 37- to 48-percent decrease in whole-water MeHg concentrations and a 37- to 48-percent reduction in whole-water THg concentrations. UltrionTM achieved a greater than 90-percent decrease in whole-water MeHg and THg concentrations.

Mercury removal from the low-particulate samples was less efficient for the sorbent materials compared to the coagulants; less than 30 percent of THg was removed from any 500-milliliter aliquot using sorbent materials. The coal-based sorbent was the most versatile of the sorbents, removing THg to a similar extent from both low-particulate source waters. The chitosan sorbent was the most effective at removing THg from the low-particulate stream sample, but less effective for the low-particulate connate-spring sample. The Hg removal efficiency of the coconut sorbent decreased quickly compared to the other two sorbents, indicating that sorption may be limited by the short contact times evaluated in this study.

California’s exposure to volcanic hazards

Released February 25, 2019 05:35 EST

2019, Scientific Investigations Report 2018-5159

Margaret Mangan, Jessica Ball, Nathan Wood, Jamie L. Jones, Jeff Peters, Nina Abdollahian, Laura Dinitz, Sharon Blankenheim, Johanna Fenton, Cynthia Pridmore

The potential for damaging earthquakes, landslides, floods, tsunamis, and wildfires is widely recognized in California. The same cannot be said for volcanic eruptions, despite the fact that they occur in the state about as frequently as the largest earthquakes on the San Andreas Fault. At least ten eruptions have taken place in the past 1,000 years, and future volcanic eruptions are inevitable.

The U.S. Geological Survey’s (USGS) national volcanic threat assessment identifies eight young volcanic areas in California as moderate, high, or very high threat. Of the eight volcanic areas that exist in California, molten rock resides beneath at least seven of these—Medicine Lake volcano, Mount Shasta, Lassen Volcanic Center, Clear Lake volcanic field, the Long Valley volcanic region, Coso volcanic field, and Salton Buttes—and are therefore considered “active” volcanoes producing volcanic earthquakes, toxic gas emissions, hot springs, geothermal systems, and (or) ground movement.

The USGS California Volcano Observatory in Menlo Park, California, monitors these potentially hazardous volcanoes to help communities and government authorities understand, prepare for, and respond to volcanic activity. Although volcanic activity can sometimes be forecast, eruptions, like earthquakes or tsunamis, cannot be prevented. Understanding the hazards and identifying what and who is in harm’s way is the first step in mitigating volcanic risk and building community resilience to volcanic hazards.

This report, which was prepared in collaboration with the California Governor’s Office of Emergency Services and the California Geological Survey, provides a broad perspective on the state’s exposure to volcanic hazards by integrating volcanic hazard information with geospatial data on at-risk populations, infrastructure, and resources. This information is intended to prompt site- and sector-specific vulnerability analyses and preparation of hazard mitigation and response plans.

Diel activity of newly metamorphosed juvenile sea lamprey (Petromyzon marinus)

Released February 22, 2019 16:51 EST

2019, PLoS ONE (14) 1-17

Scott M. Miehls, Christopher Holbrook, J. Ellen Marsden

Timing of activity, especially for juvenile anadromous fishes undertaking long migrations can be critical for survival. River-resident larval sea lamprey metamorphose into juveniles and migrate from their larval stream habitats in fall through spring, but diel timing of this migratory behavior is not well understood. Diel activity was determined for newly metamorphosed sea lamprey using day/night net sampling and passive integrated transponder (PIT) telemetry in two natural streams and PIT telemetry in an artificial stream. Downstream migration was primarily nocturnal in all studies. All but one of 372 sea lamprey were captured during night sampling in the day/night net collections and all detections (N = 56) for the in-stream PIT telemetry occurred within a few hours after sunset. Most (81% of 48) tagged lamprey moved downstream during the first night following release and moved at speeds consistent with observed water velocities. During long-term observation of behavior in the artificial stream most sea lamprey movement occurred during the night with limited occurrence of movement during daylight hours. Understanding seasonal and diel timing of downstream migration behavior may allow more effective management of sea lamprey for both conservation and control.

Upgrades to a Fortran program for estimating stream transit losses of reusable water, El Paso and Pueblo Counties, Colorado

Released February 22, 2019 14:30 EST

2019, Scientific Investigations Report 2018-5163

Susan J. Colarullo, Lisa D. Miller

In 2016, the U.S. Geological Survey, in cooperation with Pikes Peak Regional Water Authority and the Colorado Water Conservation Board, began a study to modernize a Fortran transit-loss accounting program developed by the U.S. Geological Survey to estimate net reusable flows in Fountain and Monument Creeks in El Paso and Pueblo Counties, Colorado. More than 6,000 lines of this FORTRAN77 transit-loss accounting program were revised to comply with the newer Fortran 2003 standard. The upgrade to the newer standard involved making changes in formatting and syntax on each line and, when available, adding new programming constructs that comply with the new standard. These upgrades produced a more readable Fortran program that includes safeguards to prevent accidental mistyping of variables and unintentional changes in named constants during program execution. Program revisions also introduced dynamic array allocation, whole array processing, and handling of input errors to the upgraded transit-loss accounting program.

During the upgrade from FORTRAN77 to the Fortran 2003 standard, revisions were made incrementally to the original transit-loss Fortran program. Because FORTRAN77 is a subset of Fortran 2003, the legacy FORTRAN77 statements and the upgraded Fortran 2003 statements can be compiled within the same program, permitting program revisions to be gradually phased in on a line-by-line basis. This incremental approach helped mitigate risks of introducing logic errors into the Fortran program that could produce incorrect transit-loss estimates.

Verification of the upgraded transit-loss accounting program focused on reproducing archived reusable return flows (RRF) for historical daily runs from January 5, 2015, to October 31, 2018. Because interim files storing daily streambank losses were not historically archived, no record of antecedent streambank storage losses to hydraulically connected alluvial deposits were available to provide initial conditions for each daily run. To overcome the problem of missing historical bank storage and recovery files that contain important information relating to antecedent streambank storage conditions, a 104-day “spin-up” period was required before RRFs calculated by the upgraded program and the original program matched. Estimated daily reusable return flows from archived output generated by the original program and output generated by the upgraded program were compared after this initial “spin-up” period. Daily reusable return flow estimates at delivery nodes and at the bottoms of subreaches from the upgraded Fortran program matched those output by the original program to within 0.01 and 0.0001 cubic feet per second, respectively.

Estimation of base flow on ungaged, periodically measured streams in small watersheds in western Pennsylvania

Released February 22, 2019 13:45 EST

2019, Scientific Investigations Report 2018-5150

Elizabeth Hittle, Dennis W. Risser

A 2.5-year data collection program was undertaken by the U.S. Geological Survey, in cooperation with the Pennsylvania Department of Environmental Protection (PADEP), to quantify and estimate base flow in small watersheds in western Pennsylvania where only periodic streamflow measurements had been obtained. Twelve streamgages with watershed areas of less than 10 square miles were established in western Pennsylvania for this study, with most established within Greene and Washington Counties (an area where a type of underground coal mining known as longwall mining occurs). Data from five previously established streamgages with watershed areas ranging from 48.9 to 281 square miles were also used in the analyses for this study. The index-gage method was used to relate streamflow at one streamgage referred to as the “index streamgage” to streamflow at another site of interest (usually an ungaged site, but for this study another streamgage) using a regression technique.

Streamflow regressions were developed for all newly established streamgages by using the Maintenance of Variance Extension, Type 1 (MOVE.1) method. Not all streamflow data from the newly established streamgages were used for MOVE.1 regression development; only data that have little to no influence from runoff were considered. Runoff-influenced streamflow for this study was defined as streamflow on a day that precipitation occurs plus streamflow on the following 2 days. One streamflow value per day selected from a specified schedule that captures numerous non-runoff periods was used to develop a MOVE.1 regression.

Prediction limits were calculated from the regression to provide the upper and lower bounds for the regression-produced streamflow estimates. Using these data, base flow at a site can be estimated with the index-gage method. The log10-tranformed prediction interval width and other regression diagnostics were used as indicators of regression quality when comparing streamgage relations to determine the best index streamgage among the streamgages established for this study. It was determined that index streamgages within about 10 miles of the site of interest provided the best estimated base flow and could, in the future, be used by mine operators and the PADEP to quantify base flow and to evaluate the effects of mining on streamflow.

Reimagining the potential of Earth observations for ecosystem service assessments

Released February 22, 2019 13:10 EST

2019, Science of the Total Environment (665) 1053-1063

Carlos Ramirez-Reyes, Kate A. Brauman, Rebecca Chaplin-Kramer, Gillian L. Galford, Susana B. Adamo, Christopher B. Anderson, Clarissa Anderson, Ginger R. H. Allington, Kenneth J. Bagstad, Michael T. Coe, Anna F. Cord, Laura E. Dee, Rachelle K. Gould, Meha Jain, Virginia A. Kowal, Frank E. Muller-Karger, Jessica Norriss, Peter V. Potapov, Jiangxiao Qui, Jesse T. Rieb, Brian E. Robinson, Leah H. Samberg, Nagendra Singh, Sabrina H. Szeto, Brian Voigt, Keri Watson, T. Maxwell Wright

The benefits nature provides to people, called ecosystem services, are increasingly recognized and accounted for in assessments of infrastructure development, agricultural management, conservation prioritization, and sustainable sourcing. These assessments are often limited by data, however, a gap with tremendous potential to be filled through Earth observations (EO), which produce a variety of data across spatial and temporal extents and resolutions. Despite widespread recognition of this potential, in practice few ecosystem service studies use EO. Here, we identify challenges and opportunities to using EO in ecosystem service modeling and assessment. Some challenges are technical, related to data awareness, processing, and access. These challenges require systematic investment in model platforms and data management. Other challenges are more conceptual but still systemic; they are byproducts of the structure of existing ecosystem service models and addressing them requires scientific investment in solutions and tools applicable to a wide range of models and approaches. We also highlight new ways in which EO can be leveraged for ecosystem service assessments, identifying promising new areas of research. More widespread use of EO for ecosystem service assessment will only be achieved if all of these types of challenges are addressed. This will require non-traditional funding and partnering opportunities from private and public agencies to promote data exploration, sharing, and archiving. Investing in this integration will be reflected in better and more accurate ecosystem service assessments worldwide.

Associations between environmental pollutants and larval amphibians in wetlands contaminated by energy-related brines are potentially mediated by feeding traits

Released February 22, 2019 12:57 EST

2019, Environmental Pollution (248) 260-268

Kelly L. Smalling, Chauncey W. Anderson, R. Ken Honeycutt, Isabelle M. Cozzarelli, Todd M. Preston, Blake R. Hossack

Energy production in the Williston Basin, located in the Prairie Pothole Region of central North America, has increased rapidly over the last several decades. Advances in recycling and disposal practices of saline wastewaters (brines) co-produced during energy production have reduced ecological risks, but spills still occur often and legacy practices of releasing brines into the environment caused persistent salinization in many areas. Aside from sodium and chloride, these brines contain elevated concentrations of metals and metalloids (lead, selenium, strontium, antimony and vanadium), ammonium, volatile organic compounds, hydrocarbons, and radionuclides. Amphibians are especially sensitive to chloride and some metals, increasing potential effects in wetlands contaminated by brines. We collected bed sediment and larval amphibians (Ambystoma mavortiumLithobates pipiens and Pseudacris maculata) from wetlands in Montana and North Dakota representing a range of brine contamination history and severity to determine if contamination was associated with metal concentrations in sediments and if metal accumulation in tissues varied by species. In wetland sediments, brine contamination was positively associated with the concentrations of sodium and strontium, both known to occur in oil and gas wastewater, but negatively correlated with mercury. In amphibian tissues, selenium and vanadium were associated with brine contamination. Metal tissue concentrations were higher in tadpoles that graze compared to predatory salamanders; this suggests frequent contact with the sediments could lead to greater ingestion of metal-laden materials. Although many of these metals may not be directly linked with energy development, the potential additive or synergistic effects of exposure along with elevated chloride from brines could have important consequences for aquatic organisms. To effectively manage amphibian populations in wetlands contaminated by saline wastewaters we need a better understanding of how life history traits, species-specific susceptibilities and the physical-chemical properties of metals co-occurring in wetland sediments interact with other stressors like chloride and wetland drying.

Assessing vulnerability and threat from housing development to Conservation Opportunity Areas in State Wildlife Action Plans across the United States

Released February 22, 2019 12:52 EST

2019, Landscape and Urban Planning (185) 237-245

Sarah K. Carter, Shelley S. Maxted, Tara L. E. Bergeson, David P. Helmers, Lori Scott, Volker C. Radeloff

Targeting conservation actions efficiently requires information on vulnerability of and threats to conservation targets, but such information is rarely included in conservation plans. In the U.S., recently updated State Wildlife Action Plans identify Conservation Opportunity Areas (COAs) selected by each state as priority areas for future action to conserve wildlife and habitats. The question is how threatened these COAs are by habitat loss and degradation, major threats to wildlife in the U.S. that are often caused by housing development. We compiled spatial data on COAs across the conterminous U.S. We estimated COA vulnerability using current land protection status and COA threat using projected housing growth derived from U.S. census data. COAs comprise 1–46% of each region. Across regions, 28–82% of the area within COAs is vulnerable to future housing development, and 5–55% and 7–23% of that vulnerable COA area is threatened by projected dense housing and rapid housing growth, respectively. COA vulnerability is greatest in the East. Threat from dense housing and rapid housing growth is highest in the Northeast and Pacific Southwest, respectively. Results highlight that many areas identified as important for reducing wildlife listings under the U.S. Endangered Species Act may need further protection to fulfill their conservation goals because they are both vulnerable to and threatened by future housing development. Our analyses can help practitioners target local government outreach, land protection efforts, and landscape-scale mitigation programs to decrease future COA loss from housing development, and could be expanded to address additional COA threats (e.g., wildfire, invasive species).

Kinetics of elemental sulfur reduction by petroleum hydrocarbons and the implications for hydrocarbon thermal chemical alteration

Released February 22, 2019 12:40 EST

2019, Geochimica et Cosmochimica Acta (251) 192-216

Geoffrey S. Ellis, Tongwei Zhang, Paul G. Kralert, Yongchun Tang

Although sulfur-containing compounds are known to play a significant role in the diagenic and catagenic processes that generate oil and gas, relatively little is known about the kinetics of reactions between elemental S and petroleum hydrocarbons. To investigate this subject, a series of closed-system pyrolysis experiments using paraffin, a low-sulfur oil, and a high-sulfur oil with and without elemental S were conducted, and first-order chemical kinetics were fit to the experimental results. The average value for the activation energy required to reduce elemental S to H2S and to thermochemically alter higher molecular weight hydrocarbons to methane was calculated to be 193 kJ mol-1 (46 kcal mol-1). The results of this study demonstrate that under typical geologic conditions the rate of reduction of elemental S to H2S by petroleum hydrocarbons is quite rapid. The maximum time for substantial amounts of elemental S to persist in contact with petroleum hydrocarbons is estimated to be no more than a few million years in cool reservoirs (e.g., <80 °C), and in hotter reservoirs (e.g., >120 °C) the half-life of elemental S may be as short as hundreds of years. Additionally, the presence of elemental S substantially lowers the onset temperature of hydrocarbon thermal chemical alteration (TCA). The activation energy for TCA of a low-sulfur oil to generate methane is estimated to be lowered by 92 kJ mol-1 (22 kcal mol-1) due to the presence of elemental sulfur. Consequently, the presence of elemental S in petroleum reservoirs is expected to lower the thermal stability of oil and decrease the maximum depth at which oil occurs within a basin (thermal deadline). The observed acceleration of hydrocarbon TCA is possibly due to organic sulfur compounds (e.g., thiols and sulfides) that form through the reaction of H2S or polysulfides with hydrocarbons and subsequently thermally degrade leading to the formation of sulfur radicals that in turn enhance TCA reactions.

Morphodynamics of a field of crescent-shaped rippled scour depressions: Northern Monterey Bay, CA

Released February 22, 2019 12:38 EST

2019, Marine Geology (407) 44-59

Kurt J. Rosenberger, Curt D. Storlazzi, Peter Dartnell

Despite the prevalence of rippled scour depression (RSD) on the world's continental shelves and their importance as nursery habitats for many commercially-important species, the processes responsible for their formation and geomorphic evolution are still not well understood. Most studies that focused on RSD evolution have been based on data acquired over multiple years to decades, and often during calmer summer months. Here, multiple geophysical seafloor mapping surveys of a field of RSD's off Santa Cruz, California, USA, were conducted over the course of two winters with distinctly different oceanographic forcing; these results were compared to time series oceanographic measurements made within the survey area, and put into the context of long-term trends from survey data collected during previous decades. Although the migration of these features across the seafloor occurs on decadal time scales, significant change was detected within a given year, depending on the wave climate and fluvial sediment input. RSDs shrank up to 16% or grew up to 28% in a span of a few months. Such change was predominantly the result of redistribution of fine-grained sediment input to the system by local rivers. Migration of the seafloor features appears to be the result of accumulation of fine-grained sediment at the boundary between the RSD and the surrounding fine-grained cap.

Least Bell’s Vireo (Vireo bellii pusillus) and Southwestern Willow Flycatcher (Empidonax traillii extimus) surveys in the Hansen Dam Basin, Los Angeles County, California—2018 data summary

Released February 22, 2019 08:15 EST

2019, Data Series 1103

Ryan E. Pottinger, Barbara E. Kus

Executive Summary

We surveyed for Least Bell’s Vireos (Vireo bellii pusillus; vireo) and Southwestern Willow Flycatchers (Empidonax traillii extimus; flycatcher) in cooperation with the U.S. Army Corps of Engineers along Big Tujunga Creek in the Hansen Dam Basin in Los Angeles County, California, in 2018. Four vireo surveys were conducted between April 25 and July 17, 2018, and three flycatcher surveys were conducted between May 22 and July 17, 2018. We found 77 territorial male vireos, 54 of which were confirmed as paired. Seventy-seven percent of vireos were detected in habitat characterized as mixed willow, and 84 percent of vireos were detected in habitat with greater than 50 percent native plant cover. One transient Willow Flycatcher of unknown subspecies was observed in the survey area in 2018.

Assessing lek attendance of male greater sage‐grouse using fine‐resolution GPS data: Implications for population monitoring of lek mating grouse

Released February 21, 2019 16:56 EST

2019, Population Ecology

Gregory T. Wann, Peter S. Coates, Brian G. Prochazka, John P. Severson, Adrian P. Monroe, Cameron L. Aldridge

Counts of males displaying on breeding grounds are the primary management tool used to assess population trends in lekking grouse species. Despite the importance of male lek attendance (i.e., proportion of males on leks available for detection) influencing lek counts, patterns of within season and between season variability in attendance rates are not well understood. We used high‐frequency global positioning system (GPS) telemetry data from male greater sage‐grouse (Centrocercus urophasianus; n = 67) over five lekking seasons (2013–2017) at eight study sites in Nevada to estimate lek attendance rates. Specifically, we recorded daily locations of sage‐grouse in relation to mapped lek boundaries and used generalized additive models to assess temporal variation in attendance rates by age class (subadult vs. adult). Average timing of peak attendance occurred on 16 April but varied from March 16, 2014 to April 21 , 2016. Overall, adult males attended leks at higher rates (0.683 at peak) and earlier in the season (19 March) than subadults (0.421 at peak on April 19). Peak attendance probability was positively related to cumulative winter precipitation. Daily probabilities of lek switching differed between adults (0.019 at peak on March 3) and subadults (0.046 at peak on March 22), and lek switching was negatively related to distance to nearest lek. Our results indicate variable patterns in lek attendance through time, and that lek switching may occur at higher rates than previously thought. We demonstrate the use of generalizable daily attendance curves to date‐correct lek counts and derive estimates of male abundance, although such an approach will likely require the incorporation of information on age structure to produce robust results that are useful for population monitoring.

Slough evolution and legacy mercury remobilization induced by wetland restoration in South San Francisco Bay

Released February 21, 2019 16:47 EST

2019, Estuarine, Coastal and Shelf Science (220) 1-12

Amy C. Foxgrover, Mark C. Marvin-DiPasquale, Bruce E. Jaffe, Theresa A. Fregoso

Coastal wetlands have a long history of degradation and destruction due to human development. Now recognized as one of the most productive ecosystems in the world, substantial efforts are being made to restore this critical habitat. While wetland restoration efforts are generally viewed as beneficial in terms of providing wildlife habitat and flood control, they are often accompanied by dramatic physical and chemical changes that may result in unintended consequences, which are rarely studied. Alviso Slough, a tidal slough in South San Francisco Bay, California, is the site of an ongoing effort to restore former salt-production ponds to intertidal marsh habitat. Restoration is complicated by the fact that (1) the ponds undergoing restoration are severely subsided and (2) subsurface sediments within the slough and surrounding ponds are contaminated with legacy mercury deposits. Due to concerns regarding mercury remobilization, restoration has proceeded in a cautious, methodical manner. To assess the amount of legacy mercury remobilized since restoration began, we developed a technique of combining high-resolution, biannual measurements of bathymetric scour with mercury concentration measurements from sediment cores. We estimate that 52 kg (±3) of mercury was remobilized in the 6 years since restoration began. Net bathymetric change analyses revealed seasonal trends of peak erosion during the winter months and little to no net change during summer months. Our analyses provide crucial insight on the spatial and temporal scales of geomorphic evolution within a tidal slough resulting from both natural (seasonal) variability and restoration actions. The technique presented here could be applied to other study sites and various sediment-associated contaminants of concern to aid in the design and management of restoration projects aiming to minimize negative impacts from legacy contaminants.

Evaluation of recommended revisions to Bulletin 17B

Released February 21, 2019 15:45 EST

2019, Open-File Report 2017-1064

Timothy A. Cohn, Nancy A. Barth, John F. England Jr., Beth A. Faber, Robert R. Mason Jr., Jery R. Stedinger

For the past 36 years, Bulletin 17B, published by the Interagency Committee on Water Data in 1982, has guided flood-frequency analyses in the United States. During this period, much has been learned about both hydrology and statistical methods. In keeping with the tradition of periodically updating the Bulletin 17B guidelines in light of advances in our understanding and methods, the Hydrologic Frequency Analysis Work Group (HFAWG) was charged by the Subcommittee on Hydrology (SOH) of the Advisory Committee on Water Information (ACWI) to consider possible updates to Bulletin 17B.

The purpose of this report is to consider the statistical performance of possible revisions to Bulletin 17B procedures. Of particular interest are procedures designed to accommodate more general forms of flood information. The concern is how the proposed procedures would affect the precision, accuracy and robustness of flood-frequency estimates. The investigations reported here focus on techniques for the following:

  • incorporating information related to historical flooding that occurred outside the period of systematic streamgaging; and
  • identification of potentially influential low floods (PILFs).

The proposed changes, which mostly involve generalizing Bulletin 17B’s method-of-moments procedures by using the Expected Moments Algorithm (EMA), are relatively modest, at least in the sense that they would not affect the main features of Bulletin 17B. The proposed methods include the following:

  • continued use of the log-Pearson Type 3 (LP3) distribution;
  • continued use of the Method-of-Moments fitting method applied to the logarithms of annual-peak-flow data; and
  • a generalization of the Grubbs-Beck test used in Bulletin 17B to identify low outliers. The new multiple Grubbs-Beck test is sensitive to multiple PILFs.

The hydrological literature already provides extensive support for the theory behind the proposed changes. The remaining question is practical: How well do the proposed methods perform under typical and realistic conditions and, specifically, with difficult records occasionally encountered in practice? In order to answer these questions, the HFAWG commissioned the work reported here. The following four major sets of results are provided:

  • Monte Carlo simulations of fitting procedures employing data drawn from simulated LP3 populations;
  • Monte Carlo simulations of fitting procedures employing data drawn from non-LP3 populations that were selected to reflect likely deviations of flood series from LP3 distributions, based on the experience of HFAWG members;
  • a direct comparison of the fitted LP3 distributions for 82 real “test sites” identified by an independent data group as both “typical” and “challenging” for flood-frequency estimation; and
  • simulations of fitting procedures using records obtained by resampling with replacement from the longest of the 82 test-site records.

Collectively, these studies provide a reasonably comprehensive, valid, and robust assessment of the properties of the Bulletin 17B methods and proposed alternatives. The experiments and analysis indicate that the flood quantile estimators, proposed as a revision of Bulletin 17B, do the following:

  • perform generally as well as, and in some cases much better than, Bulletin 17B estimators in terms of the mean square error of flood quantiles estimates;
  • allow for incorporation and efficient statistical treatment of broader classes of flood-frequency data and information, including historical information, binomial data and interval data; and
  • generally confirm studies and the theoretical findings reported in the hydrological literature that would support use of updated estimation procedures that have been developed since Bulletin 17B was published.

Diving behavior of Pink-footed Shearwaters Ardenna creatopus rearing chicks on Isla Mocha, Chile

Released February 21, 2019 14:11 EST

2019, Marine Ornithology: Journal of Seabird Research and Conservation (47) 17-24

Josh Adams, Jonathan J. Felis, Max Czapanskiy, Ryan D. Carle, Peter J. Hodum

Recent information reporting Pink-footed Shearwater Ardenna creatopus mortality from fisheries bycatch throughout its range has encouraged fisheries managers in Chile to evaluate and consider shearwater foraging behaviors to better evaluate risk. In response, we tracked six chickrearing adult Pink-footed Shearwaters from Isla Mocha, off south-central Chile, from 19 to 28 March 2015 using global positioning sensors and time-depth recorders. We recorded seven complete trips averaging 4.2 ± 2.5 d (mean ± SD). Chick-provisioning adults foraged within 334 km (i.e., 175 ± 100 km) of Isla Mocha. Dives (n = 515) occurred throughout the measured foraging range but most frequently occurred within 5–30 km from the mainland coast, in continental shelf waters north of Valdivia. Other regions with diving behavior were within ~20 km of Isla Mocha, and from Lebu to north of Talcahuano. Based on movement behavior analysis, adults spent most of their time at sea “resting/ foraging” (62% ± 6%), with the remainder spent “searching” (16% ± 4%) and “transiting” (20% ± 5%). The proportions of total number of dives associated with these three behaviors were similar. On average, dives were relatively shallow (1.6 ± 1.2 m, maximum depth = 10.1 m) and brief (4.7 ± 4.8 s, maximum duration = 25.7 s). Dives occurred during the day, at night, and at twilight, with most activity occurring at twilight and during the day. Although based on a small sample size, our results may be useful for informing modifications to fishing gear or fisheries policy to reduce the likelihood of bycatch and thus meet Chilean conservation goals for Pink-footed Shearwaters.

Geophysical Characterization of the heat source in the Northwest Geysers, California

Released February 21, 2019 13:50 EST

2019, Conference Paper, Proceedings, 44th Workshop on Geothermal Reservoir Engineering

Jared R. Peacock, Margaret T. Mangan, Mark Walters, Craig Hartline, Jonathan Glen, Tait E. Earney, William D. Schermerhorn

The Geysers, in northern California, is the largest energy producing geothermal field in the world. Looking to expand capacity, the operator Calpine Corporation developed an anomalously hot (~400 °C at 2.5 km depth) part of the field in the northwest Geysers, including testing of an enhanced geothermal systems (EGS). Though the area is anomalously hot, geophysical methods have failed to adequately image any inferred magmatic heat source. Gravity measurements were collected and jointly modeled with existing magnetic data along a two-dimensional profile aligned with an existing geologic cross-section. The key feature of the potential field model is a low-density, low-susceptibility body below the EGS at 5 km depth. Magnetotelluric (MT) measurements were collected around the northwest Geysers and modeled in three-dimensions to characterize subsurface resistivity structure. The resistivity model images an extension of a Quaternary granitic pluton locally known as “the felsite” under the EGS project and a possible zone of partial melt (<10%) below 7 km in the northwestern part of the field.

Rupture model of the M5.8 Pawnee, Oklahoma earthquake from regional and teleseismic waveforms

Released February 21, 2019 13:01 EST

2019, Geophysical Research Letters

Morgan P. Moschetti, Stephen H. Hartzell, R. B. Herrmann

The 2016 M5.8 Pawnee, Oklahoma earthquake is the largest earthquake to have been induced by wastewater disposal. We infer the coseismic slip history from analysis of apparent source time functions and inversion of regional and teleseismic P‐waveforms, using aftershocks as empirical Green's functions. The earthquake nucleated on the shallow part of the fault, initially rupturing towards the surface, followed shortly thereafter by slip deeper on the fault. Deeper slip occurred below the aftershocks and at greater depths than most induced seismicity in the region, suggesting that small‐ to moderate‐sized earthquakes may not occur on deeper parts of faults in Oklahoma because they are further from failure than shallower fault sections. Comparisons with models of pore pressure perturbations further suggest that the earthquake may have initiated within a region of higher pore pressure perturbation but was not confined to this zone. These observations inform source physics and understanding of maximum magnitudes.

Estimating sand concentrations using ADCP‐based acoustic inversion in a large fluvial system characterized by bi‐modal suspended‐sediment distributions

Released February 21, 2019 11:11 EST

2019, Earth Surface Processes and Landforms

Ricardo N. Szupiany, Cecilia Lopez Weibel, Massimo Guerrero, Francisco Latosinski, Molly S. Wood, Lucas Dominguez Ruben, Kevin Oberg

Quantifying sediment flux within rivers is a challenge for many disciplines due, mainly, to difficulties inherent to traditional sediment sampling methods. These methods are operationally complex, high cost, and high risk. Additionally, the resulting data provide a low spatial and temporal resolution estimate of the total sediment flux, which has impeded advances in the understanding of the hydro‐geomorphic characteristics of rivers. Acoustic technologies have been recognized as a leading tool for increasing the resolution of sediment data by relating their echo intensity level measurements to suspended sediment. Further effort is required to robustly test and develop these techniques across a wide range of conditions found in natural river systems. This article aims to evaluate the application of acoustic inversion techniques using commercially available, down‐looking acoustic Doppler current profilers (ADCPs) in quantifying suspended sediment in a large sand bed river with varying bi‐modal particle size distributions, wash load and suspended‐sand ratios, and water stages. To achieve this objective, suspended sediment was physically sampled along the Paraná River, Argentina, under various hydro‐sedimentological regimes. Two ADCPs emitting different sound frequencies were used to simultaneously profile echo intensity level within the water column. Using the sonar equation, calibrations were determined between suspended‐sand concentrations and acoustic backscatter to solve the inverse problem. The study also analyzed the roles played by each term of the sonar equation, such as ADCP frequency, power supply, instrument constants, and particle size distributions typically found in sand bed rivers, on sediment attenuation and backscatter. Calibrations were successfully developed between corrected backscatter and suspended‐sand concentrations for all sites and ADCP frequencies, resulting in mean suspended‐sand concentration estimates within about 40% of the mean sampled concentrations. Noise values, calculated using the sonar equation and sediment sample characteristics, were fairly constant across evaluations, suggesting that they could be applied to other sand bed rivers.

Assessing the impact of the Conservation Reserve Program on honey bee health

Released February 21, 2019 10:46 EST

2019, Fact Sheet 2018-3082

Clint R. V. Otto

Insect pollinators are critically important for maintaining U.S. food production and ecosystem health. The upper Midwest is home to more than 40 percent of all U.S. honey bee colonies and is considered by many beekeepers to be America’s last beekeeping refuge. Beekeepers come to this region because their honey bees require high-quality grassland and bee-friendly agricultural crops to make honey and to improve bee health. Agricultural grassland, such as those enrolled in the Conservation Reserve Program (CRP), support flowers that provide bees with the pollen and nectar they need. In 2014, the U.S. Department of Agriculture (USDA) and the U.S. Geological Survey (USGS) formed a partnership to assess the impact of the CRP on honey bee health and determine how the cost-effectiveness of the CRP could be improved to promote pollinator habitat. This USGS assessment has generated important findings that could improve USDA’s program delivery and demonstrates the importance of the CRP to honey bees, beekeepers, agricultural producers, and the public.

Evaluation of Chinook salmon (Oncorhynchus tshawytscha) fry survival at Lookout Point Reservoir, western Oregon, 2017

Released February 21, 2019 08:44 EST

2019, Open-File Report 2019-1011

Tobias J. Kock, Russell W. Perry, Gabriel S. Hansen, Philip V. Haner, Adam C. Pope, John M. Plumb, Karen M. Cogliati, Amy C. Hansen

A field study was conducted to estimate survival of fry-sized juvenile Chinook salmon (Oncorhynchus tshawytscha) in Lookout Point Reservoir, western Oregon, during 2017. The field study consisted of releasing three groups of genetically marked fish in the reservoir and monthly fish sampling. Fish were released during April 18–19 (43,950 fish), May 30–June 2 (44,145 fish), and on June 28, 2017 (3,920 fish). Reservoir sampling began in May and occurred monthly through October, consisting of 5-day events where juvenile Chinook salmon were collected using various gear types (electrofishing, shoreline traps, gill nets). Data were analyzed using two models: (1) a staggered release-recovery model (SRRM), and (2) a parentage-based tagging (PBT) N-mixture model. The SRRM provided survival estimates from two periods: (1) mid-April to late May (SSRRM1), and (2) late May to late June (SSRRM2). Multiple estimates of survival were possible for each period using different combinations of recovery data from the three groups of fish that were released. Survival estimates for SSRRM1 ranged from 0.470 to 0.520. Estimates for SSRRM2 ranged from 0.968 to 0.969; cumulative survival from mid-April to late June (SSRRM2) was estimated at 0.870. We suspect that issues with the third release group led to biased survival results using the SRRM. The PBT N-mixture model provided survival estimates from six periods: (1) mid-April to mid-May (SNMIX1), (2) mid-May to mid-June (SNMIX2), (3) mid-June to mid-July (SNMIX3), (4) mid-July to mid-August (SNMIX4), (5) mid-August to mid-September (SNMIX5), and (6) mid-September to mid-October (SNMIX6). Survival estimates from the PBT N-mixture model were lowest for SNMIX1 (0.461) and increased monthly to a high of 0.970 for SNMIX6. Cumulative survival from mid-April to mid-July was 0.233 and overall survival from mid-April to mid-October was 0.188. This suggests that most mortality occurred early in the study when juvenile Chinook salmon were small. This could be because these fish were most vulnerable to predation in the reservoir at that time. We determined that mortality of juvenile Chinook salmon was high in the reservoir during this study and similar estimates of parr-to-smolt survival have been observed in other systems. Additional analyses are required, including results from the second year of study (2018), and potentially similar evaluations will need to be made at other locations to determine if reservoir mortality is a limiting survival factor for Chinook salmon in the Middle Fork Willamette River.

Using the Distinct Population Segment concept to protect fishes with low levels of genomic differentiation: conservation of an endemic minnow (Hitch, Lavinia exilicauda)

Released February 20, 2019 16:17 EST

2019, Transactions of the American Fisheries Society (148) 406-416

Jason Baumsteiger, Matthew Young, Peter B. Moyle

In the United States, the Endangered Species Act (ESA) of 1973 was enacted to conserve species which are endangered or threatened throughout all or a portion of their range. The definition of ‘species’ includes subspecies and distinct population segments (DPSs). In freshwater fishes, use of DPS designations has largely been restricted to salmonid fishes (Salmonidae), although the DPS concept is increasingly applied to other fishes as well. As more taxa approach threatened status, the difficult question becomes what to do when genetic evidence does not strongly support formal taxonomic designations (full species or subspecies). We examine the potential use of the DPS concept to protect fishes using the example of Hitch (Lavinia exilicauda), a cyprinid fish endemic to California. The Hitch is divided up into three formally described, geographically separated subspecies. However, genomic studies (RADseq), presented here with three independent analyses using a large data set, only weakly support subspecies designations. Results suggest population but not subspecies structure. Nevertheless, conventional taxonomic methods, strong contemporary isolation, the importance of protecting genetic diversity, and high cultural values still qualify all three designated subspecies for DPS status and demonstrate how taxa such as Clear Lake Hitch can warrant protection under the ESA.

Organic geochemical investigation of far‐field tsunami deposits of the Kahana Valley, O'ahu, Hawai'i

Released February 20, 2019 16:15 EST

2019, Sedimentology

Piero Bellanova, Mike Frenken, Bruce M. Richmond, Jan Schwarzbauer, Seanpaul La Selle, Frances Griswold, Bruce E. Jaffe, Alan R. Nelson, Klaus Reicherter

Far‐field tsunami deposits observed in the Kahana Valley, O'ahu, Hawai'i (USA), were investigated for their organic‐geochemical content. During short high‐energy events, (tsunamis and storms) organic and chemical components are transported with sediment from marine to terrestrial areas. This study investigates the use of anthropogenic based organic geochemical compounds (such as polycyclic aromatic hydrocarbons, pesticides and organochlorides) as a means to identify tsunami deposits. Samples were processed by solid‐liquid extraction and analyzed using gas chromatography–mass spectrometry. A total of 21 anthropogenic marker compounds were identified, of which 11 compounds were selected for detailed analysis. Although the tsunami deposits pre‐date industrial activity in Hawaii by several hundred years, distinct changes were found in the concentrations of anthropogenic marker compounds between sandy tsunami deposits and the surrounding mud/peat layers, which may help in identifying tsunami deposits within cores. As expected, low overall concentrations of anthropogenic markers and pollutants were observed due to the lack of industrial input‐sources and little anthropogenic environmental impact at the study site. This geochemical characterization of tsunami deposits shows that anthropogenic markers have significant potential as another high‐resolution, multi‐proxy method for identifying tsunamis in the sedimentary record.

Sediment trapping and carbon sequestration in floodplains of the lower Atchafalaya Basin, LA: Allochthonous vs. autochthonous carbon sources

Released February 20, 2019 16:10 EST

2019, Journal of Geophysical Research: Biogeosciences

Cliff R. Hupp, Daniel E. Kroes, Gregory B. Noe, Edward R. Schenk, Richard H. Day

Recent studies suggest that about 2 Pg of organic C is stored on floodplains worldwide. The present study indicates the Atchafalaya River, fifth largest river in the United States in terms of discharge, traps 30 mm/y of sediment on average within its floodplain, which is the highest average non‐episodic rate of fluvial deposition on the U.S. Coastal Plain. We installed sediment sampling stations at 23 sites, normally in transect, in the Atchafalaya Basin; these sites represent the range of hydrogeomorphic conditions on the floodplain based on hydrologic connectivity with the river main stem. The rate of sedimentation translates into about 12.5 Tg/y and includes 694 Mg/y of organic C. Highest sedimentation rates are associated with areas of high connectivity to channels and prograding deltaic processes. The δ13C content suggests that 35% of deposited C is derived from river‐suspended sediment compared to litterfall in the Basin. Thus, much of the organic C sequestered is allochthonous material. However, isolated interior sites with limited connectivity to the channel may generate and sequester large amounts of autochthonous C. The substantial trapping of both auto‐ and allochthonous C (392 Mg/y) make this freshwater‐forested floodplain critical in storage of material before reaching the coastal delta and estuary. This C deposition rate (340 g C m‐2y‐1) exceeds all other rates reported in recent Blue Carbon and Tidal Freshwater Forested Wetland studies. Atchafalaya C sequestration occurs in/near areas with tidal influence and like other coastal systems is an important site for trapping mineral and organic sediment and in global C cycling.

Stochastic model for simulating Souris River Basin regulated streamflow upstream from Minot, North Dakota

Released February 20, 2019 12:45 EST

2019, Scientific Investigations Report 2018-5155

Kelsey A. Kolars, Aldo V. Vecchia, Joel M. Galloway

The Souris River Basin is a 24,000 square-mile basin in the Provinces of Saskatchewan and Manitoba in Canada, and the State of North Dakota in the United States. Above-average snowpack during the winter of 2010–11, along with record-setting rains in May and June of 2011, led to record flooding that caused extensive damage to Minot, North Dakota, and numerous smaller communities in Saskatchewan, Manitoba, and North Dakota. As a result, the International Souris River Board created the Souris River Flood Task Force to evaluate potential reservoir operation changes and flood control measures to manage future floods and droughts. Part of this evaluation involved identifying a need for a stochastic streamflow model to estimate the likelihood of future flooding or drought.

A stochastic natural (unregulated) streamflow simulation model described in a previous report was built upon in this report to include the effects of regulation of four reservoirs (Rafferty, Alameda, and Boundary Reservoirs and Lake Darling) and their operation guidelines. First, a regulated reservoir storage/streamflow routing model was developed and calibrated from when all four reservoirs were in operation until the end of the reconstructed natural streamflow dataset provided by the U.S. Army Corps of Engineers (1992–2011). The regulated reservoir storage/streamflow routing model then was combined with the stochastic natural (unregulated) streamflow model to provide a stochastic regulated streamflow simulation model for the Souris River Basin upstream from Minot, North Dakota.

The stochastic regulated streamflow simulation model was used to estimate regulated flood frequency curves, which are useful for feasibility and design of critical structures such as levees or bridges. Three potential future climatic conditions were considered in this analysis: condition A (wet equilibrium), representing wet (similar to 1970–2017) climatic conditions; condition B (transition), representing transition from wet to dry (similar to 1912–69) climatic conditions; and condition C (dry equilibrium), representing dry climatic conditions. Comparison of the estimated flood frequency curves for regulated flow among the three climatic conditions indicated large differences in flood magnitudes for the more extreme (1-percent or less) annual exceedance probabilities. The estimated 0.2-percent annual exceedance probability flood magnitude for the Souris River upstream from Minot, N. Dak., was 29,300 cubic feet per second for condition A (wet equilibrium), compared to 14,800 cubic feet per second for condition C (dry equilibrium). For comparison, the recorded peak streamflow for 2011 for the Souris River upstream from Minot, N. Dak., was 26,900 cubic feet per second. Although it is not possible to predict how long the current (1970–2017) wet climatic conditions may persist, flood risk for at least the next 25 years, or until about 2040, may be represented best by climatic condition A.

Assessing causes of mortality for endangered juvenile Lost River suckers (Deltistes luxatus) in mesocosms in Upper Klamath Lake, south-central Oregon, 2016

Released February 20, 2019 12:32 EST

2019, Open-File Report 2019-1006

Danielle M. Hereford, Carla M. Conway, Summer M. Burdick, Diane G. Elliott, Todd M. Perry, Amari Dolan-Caret, Alta C. Harris

Executive Summary

The recovery of endangered Lost River suckers (Deltistes luxatus) in Upper Klamath Lake, south-central Oregon, has been impeded because juveniles are not recruiting into adult spawning populations. Adult sucker populations spawn each spring but mortality of age-0 suckers during their first summer is excessively high, and recruitment of juveniles into adult populations does not occur in most years. The last significant year class to join spawning aggregations was hatched in 1991. Capture rates for age-0 Lost River suckers decrease so substantially each summer that it is thought that mortality is nearly 100 percent within the first year of life each year. Causes of mortality are not understood but poor water quality, parasites, disease, predation, and non-native species are suspected to contribute to mortality. Upper Klamath Lake is hypereutrophic and summer water-quality conditions have large diurnal and seasonal fluctuations. Photosynthesis of Aphanizomenon flos-aquae, the most abundant cyanobacterium in Upper Klamath Lake, is responsible for large fluctuations in dissolved-oxygen (DO) concentrations and pH.

We introduced hatchery-raised, passive integrated transponder-tagged juvenile Lost River suckers into large mesocosms located at Fish Banks, Mid North, and Rattlesnake Point in Upper Klamath Lake, Oregon, to assess sucker mortality relative to water-quality conditions. We identified the date of death for each sucker by assessing movement patterns among vertically stratified antennas. We modeled daily mortality using known fate models relative to water-quality conditions measured by sondes. Histopathology was used to understand causes of eminent mortality for moribund suckers.

Fish mortality, growth, health, and movement patterns varied among locations, but it was unclear whether this variation was due to water-quality or other factors. Seasonal mortality was 58.8 percent at Fish Banks, 27.4 percent at Mid North, and 11.5 percent at Rattlesnake Point. Growth over the 109-day study period was lowest at Fish Banks (34.5 ±10.0 millimeters [mm] standard length (SL); 18.6 ±7.7 grams [g]), intermediate at Mid North (57.5 ±13.6 mm SL; 40.1 ±15.4 g), and greatest at Rattlesnake Point (78.4 ±13.0 mm SL; 72.5 ±18.7 g). Our ability to assess causes of juvenile sucker mortality in mesocosms using our modelling approach was limited by low daily mortality. Zero to 3 mortalities occurred per day, except on July 30 at Fish Banks when 7 mortalities occurred. Relative to any other measured and tested water-quality condition, mortality was more likely to occur on days with large fluctuations in oxygen percent saturation. When we assessed the fit of the most parsimonious model, performance was poor, which suggested that other factors were contributing to mortality. Our ability to assess the relationship between seasonal patterns in water quality and fish mortality were limited by the absence of substantial differences in water quality among sites, inconsistency in the depth at which measurements were collected, and no clear pattern in conditions leading up to and during mortality events. Except for DO at Rattlesnake Point and diel temperature variations at Fish Banks, seasonally summarized water-quality factors were similar among sites. The locations of water-quality monitors within the water column likely explain the differences in DO at Rattlesnake Point and temperature variation at Fish Banks. Furthermore, DO concentrations and other water-quality factors occurring during and prior to mortality events were inconsistent.

Microscopic assessments indicated severe gill hyperplasia, fusion of the secondary lamellae, and severe Ichthyobodo sp. infestations on the gills of most moribund suckers. Liver glycogen was usually depleted in suckers with severe Ichthyobodo sp. infestations. Ichthyobodo sp. infestations probably were the immediate cause of death and probably originated from the Klamath Tribes Fish Research Facility, although this parasite also is present in Upper Klamath Lake and severe water-quality conditions may have contributed to morbidity. As suckers in the mesocosms died, they were replaced with suckers from the Fish Research Facility that likely were heavily parasitized with Ichthyobodo sp. Therefore, it is possible that the gradient in mortality rate among sites was owing to site-varying differences in inadvertent increases in introduced parasite loads.

Hydraulic and water-quality indicators of aquifer zones contributing groundwater flow to wells in the Santa Fe Group aquifer system near southeast Albuquerque, New Mexico, 2013–16

Released February 20, 2019 12:03 EST

2019, Scientific Investigations Report 2018-5138

Rebecca E. Travis, Nathan C. Myers

An ethylene dibromide (EDB) plume extends approximately 5,880 feet northeast from the Bulk Fuels Facility on Kirtland Air Force Base. The leading edge of the EDB plume is about 3,700 feet upgradient from several water-supply wells. The water-supply wells are screened in the upper Santa Fe Group aquifer system. Within the upper Santa Fe Group, two primary clay-rich layers, the A1 and A2 units, separate water-producing zones. The U.S. Geological Survey, in cooperation with the Albuquerque Bernalillo County Water Utility Authority and the U.S. Air Force, installed four sentinel well nests and two aquifer-test pumping wells between the EDB plume and the water-supply wells. The purpose of the sentinel wells is to provide early warning of EDB plume migration towards water-supply wells. The sentinel well nests include at least three wells that are screened above, in between, and below the A1 and A2 units. The two aquifer-test pumping wells, installed for performing hydraulic tests on the aquifer system, are screened across both clay layers, as are the nearby water-supply wells. Well-bore flow logging indicated that greater than 60 percent of groundwater flow to the wells was through the deepest interval below the lowermost clay layer (A1 unit). The interval between the A1 and A2 units is the second most productive interval. Water-quality data also indicated that water drawn from the aquifer-test pumping wells and previously studied nearby water-supply wells is most similar in composition to water from the sentinel wells screened in the middle and deep intervals.

Hydrodynamic controls on sediment retention in an emerging diversion-fed delta

Released February 20, 2019 11:52 EST

2019, Geomorphology (332) 100-111

Molly E. Keogh, Alexander S. Kolker, Gregg A. Snedden, Alisha A. Renfro

The morphodynamics of river-dominated deltas are largely controlled by the supply and retention of sediment within deltaic wetlands and the rate of relative sea-level rise. Yet, sediment budgets for deltas are often poorly constrained. In the Mississippi River Delta, a system rapidly losing land due to natural and anthropogenic causes, restoration efforts seek to build new land through the use of river diversions. At the Davis Pond Freshwater Diversion, a new crevasse splay has emerged since construction was completed in 2002. Here, we use beryllium-7 activity in sediment cores and USGS measurements of discharge and turbidity to calculate seasonal sediment input, deposition, and retention within the vegetated Davis Pond receiving basin. In winter/spring 2015, which included an experimental period of high discharge through the diversion, Davis Pond received 106,800 metric tons of sediment, 44% of which was retained within the basin. During this time, mean flow velocity was 0.21 m s−1 and mean turbidity was 56 formazin nephelometric units (FNU). In summer/fall 2015, the Davis Pond basin received 35,900 metric tons of sediment, 81% of which was retained. Mean flow velocity in summer/fall was 0.10 m s−1 and mean turbidity was 55 FNU. The increase in sediment retention from winter/spring 2015 to summer/fall 2015 may be due in part to the corresponding drop in water flow velocity, which allowed more sediment to settle out of suspension. Although high water discharge increases sediment input and deposition, increased turbulence associated with higher current velocity appears to increase sediment throughput and thereby decrease the sediment trapping efficiency. Sediment retention in Davis Pond is on the high end of the range seen in deltaic wetlands, perhaps due to the enclosed geometry of the receiving basin. Future diversion design and operation should target moderate water discharge and flow velocities in order to jointly maximize sediment deposition and retention and provide optimal conditions for delta growth.

The potential role of very high-resolution imagery to characterise lake, wetland and stream systems across the Prairie Pothole Region, United States

Released February 20, 2019 10:47 EST

2019, International Journal of Remote Sensing

Melanie K. Vanderhoof, Charles R. Lane

Aquatic features critical to watershed hydrology range widely in size from narrow, shallow streams to large, deep lakes. In this study we evaluated wetland, lake, and river systems across the Prairie Pothole Region to explore where pan-sharpened high-resolution (PSHR) imagery, relative to Landsat imagery, could provide additional data on surface water distribution and movement, missed by Landsat. We used the monthly Global Surface Water (GSW) Landsat product as well as surface water derived from Landsat imagery using a matched filtering algorithm (MF Landsat) to help consider how including partially inundated Landsat pixels as water influenced our findings. The PSHR outputs (and MF Landsat) were able to identify ~60–90% more surface water interactions between waterbodies, relative to the GSW Landsat product. However, regardless of Landsat source, by documenting many smaller (<0.2 ha), inundated wetlands, the PSHR outputs modified our interpretation of wetland size distribution across the Prairie Pothole Region.

Dynamic N-mixture models with temporal variability in detection probability

Released February 20, 2019 10:44 EST

2019, Ecological Modelling (393) 20-24

Qing Zhao, J. Andrew Royle

In theory parameters of dynamic N-mixture models can be estimated with multiple years of data without the robust design under the assumption of constant detection probability. However, such an assumption can rarely be met in long-term studies, and the consequences of violating this assumption in the inferences of dynamic N-mixture models have not been assessed. In this study we used simulation studies to evaluate inferences of the original dynamic N-mixture model and two of its spatial extensions in the face of temporal variability in detection probability. We first evaluated the dynamic N-mixture models when detection probability that varied temporally was wrongly treated as a constant. We then evaluated if the robust design was necessary for dynamic N-mixture models to provide valid parameter estimates when detection probability was correctly assumed to vary temporally. Our results showed that, when detection probability that varied temporally was wrongly treated as a constant, biases were introduced in the parameter estimates of dynamic N-mixture models. When detection probability was correctly assumed to vary temporally, the models could provide valid parameter estimates with the robust design. The model could also provide valid parameter estimates when detection probability was a random effect, even without the robust design. Based on our results, we strongly recommended considering temporal variability in detection probability when using dynamic N-mixture models to analyze long-term data and adopting the robust design in long-term surveys. Our work here is not only useful for data analysis but also important for research design, and thus are relevant to a wide range of studies.

Oxygen isotopic investigation of silicic magmatism in the Stillwater caldera complex, Nevada: Generation of large-volume, low-δ18O rhyolitic tuffs and assessment of their regional context in the Great Basin of the western United States

Released February 19, 2019 16:28 EST

2019, GSA Bulletin

Kathryn E. Watts, David A. John, Joseph P. Colgan, Christopher D. Henry, Ilya N. Bindeman, John W. Valley

Successive caldera-forming eruptions from ca. 30 to 25 Ma generated a large nested caldera complex in western Nevada that was subsequently dissected by Basin and Range extension, providing extraordinary cross-sectional views through diverse volcanic and plutonic rocks. A high-resolution oxygen isotopic study was conducted on units that represent all major parts of the Job Canyon, Louderback Mountains, Poco Canyon, and Elevenmile Canyon caldera cycles (29.2−25.1 Ma), and several Cretaceous plutons that flank the Stillwater caldera complex. We provide new oxygen and strontium isotope data for 12 additional caldera centers in the Great Basin, which are synthesized with >150 published oxygen and strontium isotope analyses for regional Mesozoic basement rocks. Stillwater zircons span a large isotopic range (δ18Ozircon of 3.6‰−8.2‰), and all caldera cycles possess low-δ18O zircons. In some cases, they are a small proportion of the total populations, and in others, they dominate, such as in the low-δ18O rhyolitic tuffs of Job Canyon and Poco Canyon (δ18Ozircon = 4.0‰−4.3‰; δ18Omagma = 5.5‰−6‰). These are the first low-δ18O rhyolites documented in middle Cenozoic calderas of the Great Basin, adding to the global occurrence of these important magma types that fingerprint recycling of shallow crust altered by low-δ18O meteoric waters. The appearance of low-δ18O rhyolites in the Stillwater caldera complex is overprinted on a Great Basin−wide trend of miogeoclinal sediment contribution to silicic magmas that elevates δ18O compositions, making identification of 18O depletions difficult. Though not a nominally low-δ18O rhyolite, the tuff of Elevenmile Canyon possesses both low-δ18O and high-δ18O zircon cores that are overgrown by homogenized zircon rims that approximate the bulk zircon average, pointing to batch assembly of isotopically diverse upper crustal melts to generate one of the most voluminous (2500−5000 km3) tuff eruptions in the Great Basin. Despite overlapping in space and time, each caldera-forming cycle of the Stillwater complex has a unique oxygen isotope record as retained in single zircons. Most plutons that were spatially and temporally coincident with calderas have isotopic compositions that diverge from the caldera-forming tuffs and cannot be their cogenetic remnants.

Complex immune responses and molecular reactions to pathogens and disease in a desert reptile (Gopherus agassizii)

Released February 19, 2019 16:23 EST

2019, Ecology and Evolution (9) 2516-2534

K. Kristina Drake, Christina M. Aiello, Lizabeth Bowen, Rebecca L. Lewison, Todd C. Esque, Kenneth E. Nussear, Shannon C. Waters, Peter J. Hudson

Immune function plays an important role in an animal's defense against infectious disease. In reptiles, immune responses may be complex and counterintuitive, and diagnostic tools used to identify infection, such as induced antibody responses are limited. Recent studies using gene transcription profiling in tortoises have proven useful in identifying immune responses to various intrinsic and extrinsic stressors. As part of a larger experiment with Mojave desert tortoises (Gopherus agassizii), we facilitated the transmission of the pathogenic bacteria, Mycoplasma agassizii (Myag), to naïve adults and measured innate and induced immune reactions over time. Specifically, we evaluated clinical condition, presence of Myag in the nasal/oral cavity, induced antibody responses specific to Myag, and measured molecular reactions (gene transcript profiles) in 15 captive tortoises classified as naïve, exposed, or infected and 14 wild tortoises for comparison. Myag was confirmed inside the nasal/oral cavity in exposed tortoises within 30–60 days of introduction to infected animals, yet we did not detect Myag specific induced antibody responses in these individuals until 420–595 days post exposure. Surprisingly, we found no overall differences in the gene transcript profiles between our experimental treatment groups throughout this study. This work highlights the complexities in assessing immune function and diagnosing pathogen related infections in tortoises and other reptiles.

Phylogeography and evolution of infectious hematopoietic necrosis virus in China

Released February 19, 2019 16:20 EST

2019, Molecular Phylogenetics and Evolution (131) 19-28

Liming Xu, Jingzhuang Zhao, Miao Liu, Gael Kurath, Rachel B. Breyta, Guangming Ren, Jiasheng Yin, Hongbai Liu, Tongyan Lu

Infectious hematopoietic necrosis virus (IHNV) is a well-known rhabdoviral pathogen of salmonid fish. In this study, a comprehensive analysis of 40 IHNV viruses isolated from thirteen fish farms in nine geographically dispersed Chinese provinces during 2012 to 2017 is presented. Identity of nucleotide and amino acid sequences among all the complete glycoprotein (G) genes from Chinese isolates was 98.0–100% and 96.7–100%, respectively. Coalescent phylogenetic analyses revealed that all the Chinese IHN virus characterized in this study were in a monophyletic clade that had a most recent common ancestor with the J Nagano (JN) subgroup within the J genogroup of IHNV. Within the Chinese IHNV clade isolates obtained over successive years from the same salmon fish farm clustered in strongly supported subclades, suggesting maintenance and diversification of virus over time within individual farms. There was also evidence for regional virus transmission within provinces, and some cases of longer distance transmission between distant provinces, such as Gansu and Yunnan. The data demonstrated that IHNV has evolved into a new subgroup in salmon farm environments in China, and IHNV isolates are undergoing molecular evolution within fish farms. We suggest that Chinese IHNV comprises a separate JC subgroup within the J genogroup of IHNV.

User’s guide for Assessment Tract Aggregation GUI (ATA GUI)—A graphical user interface for the AggtEx.fn R script

Released February 19, 2019 15:15 EST

2019, Techniques and Methods 7-C21

Jason L. Shapiro, Gilpin R. Robinson Jr.

The U.S. Geological Survey three-part method for mineral resource assessments estimates numbers of undiscovered mineral deposits as probability distributions in geologically defined regions termed “permissive tracts.” This report describes a graphical user interface (GUI) script developed in open-source statistical software (R) that aggregates estimated undiscovered deposits of a given type from two or more permissive tracts using the AggtEx.fn R script. The AggtEx.fn R script aggregates undiscovered deposit estimates assuming independence, total dependence, or some degree of correlation among aggregated areas, given a user-specified correlation matrix. The script outputs three sets of aggregated estimates based on those three assumptions.

The GUI script described in this report, Assessment Tract Aggregation GUI (ATA GUI), provides an easy-to-use tool that supports implementation of the AggtEx.fn R script, installation of the R packages needed to run the application, and creation of a combined input file from individual files generated by the MapMark4GUI software. Users can also use EMINERS output information by creating a file of output values following the MapMark4GUI output file format. The probabilistic estimates of aggregated undiscovered deposits produced by ATA GUI can be used as input for MapMark4GUI to estimate contained resources for the aggregated tracts. MapMark4GUI uses Monte Carlo simulation to combine undiscovered deposit estimates with tonnage and grade models to simulate undiscovered mineral resources for a region of interest. This simulation includes the amounts of commodities and rock that could be present within a permissive tract. This report includes instructions on installing and running the ATA GUI script and describes the input and output files used and created during the aggregation process.

Occupancy models for citizen-science data

Released February 19, 2019 13:21 EST

2019, Methods in Ecology and Evolution (10) 8-21

Res Altwegg, James D. Nichols

  1. Large‐scale citizen‐science projects, such as atlases of species distribution, are an important source of data for macroecological research, for understanding the effects of climate change and other drivers on biodiversity, and for more applied conservation tasks, such as early‐warning systems for biodiversity loss.
  2. However, citizen‐science data are challenging to analyse because the observation process has to be taken into account. Typically, the observation process leads to heterogeneous and non‐random sampling, false absences, false detections, and spatial correlations in the data. Increasingly, occupancy models are being used to analyse atlas data.
  3. We advocate a dual approach to strengthen inference from citizen science data for the questions the programme is intended to address: (a) the survey design should be chosen with a particular set of questions and associated analysis strategy in mind and (b) the statistical methods should be tailored not only to those questions but also to the specific characteristics of the data.
  4. We review the consequences of particular survey design choices that typically need to be made in atlas‐style citizen‐science projects. These include spatial resolution of the sampling units, allocation of effort in space, and collection of information about the observation process. On the analysis side, we review extensions of the basic occupancy models that are frequently necessary with atlas data, including methods for dealing with heterogeneity, non‐independent detections, false detections, and violation of the closure assumption.
  5. New technologies, such as cell‐phone apps and fixed remote detection devices, are revolutionizing citizen‐science projects. There is an opportunity to maximize the usefulness of the resulting datasets if the protocols are rooted in robust statistical designs and data analysis issues are being considered. Our review provides guidelines for designing new projects and an overview of the current methods that can be used to analyse data from such projects.

Per- and polyfluoroalkyl substances (PFAS) in plasma of the West Indian manatee (Trichechus manatus)

Released February 19, 2019 13:14 EST

2019, Marine Pollution Bulletin (140) 610-615

Kady Palmer, Jacqueline T. Bangma, Jessica L. Reiner, Robert K. Bonde, Jeffrey E. Korte, Ashley S. P. Boggs, John A. Bowden

Per- and polyfluoroalkyl substances (PFAS) are ubiquitous, synthetic anthropogenic chemicals known to infiltrate and persist in biological systems as a result of their stability and bioaccumulation potential. This study investigated 15 PFAS, including short-chain carboxylic and sulfonic acids, and their presence in a threatened herbivore, the West Indian manatee (Trichechus manatus). Seven of the 15 PFAS examined were detected in manatee plasma. Perfluorooctanesulfonic acid (PFOS) (ranging from 0.13 to 166 ng/g ww) and perfluorononanoic acid (PFNA) (ranging from 0.038 to 3.52 ng/g ww) were detected in every manatee plasma sample examined (n = 69), with differing medians across sampling sites in Florida, Crystal River (n = 39), Brevard County (n = 18), Everglades National Park (n = 8), and four samples (n = 4) from Puerto Rico. With an herbivorous diet and long life-span, the manatee provides a new perspective to monitoring PFAS contamination.

Physical mechanisms influencing localized patterns of temperature variability and coral bleaching within a system of reef atolls

Released February 19, 2019 12:28 EST

2019, Coral Reefs

Rebecca H. Green, Ryan J. Lowe, Mark L. Buckley, Taryn Foster, James Gilmour

Interactions between oceanic and atmospheric processes within coral reefs can significantly alter local-scale (< km) water temperatures, and consequently drive variations in heat stress and bleaching severity. The Scott Reef atoll system was one of many reefs affected by the 2015–2016 mass coral bleaching event across tropical Australia, and specifically experienced sea surface temperature anomalies of 2 °C that caused severe mass bleaching (> 60%) over most of this system; however, the bleaching patterns were not uniform. Little is known about the processes governing thermodynamic variability within atolls, particularly those that are dominated by large amplitude tides. Here, we identify three mechanisms at Scott Reef that alleviated heat stress during the marine heatwave in 2016: (1) the cool wake of a tropical cyclone that induced temperature drops of 1.3 °C over a period of 8 days; (2) air–sea heat fluxes that interacted with the reef morphology during neap tides at one of the atolls to reduce water temperatures by up to 2.9 °C; (3) internal tidal processes that forced deeper and cooler water (up to 2.7 °C) into some sections of the shallow reefs. The latter two processes created localized areas of reduced temperatures that led to lower incidences of coral bleaching for parts of the reef. We predict these processes are likely to occur in other similar tide-dominated reef environments worldwide. Identifying locations where physical processes reduce heat stress will likely be critical for coral reefs in the future, by maintaining communities that can help facilitate local recovery of reefs following bleaching events that are expected to increase in frequency and severity in the coming decades.

Carbon dioxide mineralization feasibility in the United States

Released February 19, 2019 12:15 EST

2019, Scientific Investigations Report 2018-5079

Madalyn S. Blondes, Matthew D. Merrill, Steven T. Anderson, Christina A. DeVera

Geologic carbon dioxide (CO2) storage is one of many methods for stabilizing the increasing concentration of CO2 in the Earth’s atmosphere. The injection of CO2 in deep subsurface sedimentary reservoirs is the most commonly discussed method; however, the potential for CO2 leakage can create long-term stability concerns. This report discusses the feasibility of an alternative form of geologic CO2 storage: CO2 mineralization. In this method, CO2 reacts with rocks and minerals to form solid and stable carbonate rocks. New pilot projects and laboratory-based kinetics experiments have revealed that this method, both in situ and ex situ, may be a viable option for storage. In situ storage targets in-place rocks at the surface or subsurface. Ex situ storage targets industrial byproducts at the surface like mine tailings. Environmental risks include induced seismicity for in situ methods if pressure is not managed properly, as well as potential water and land use effects. However, there are fewer long-term CO2-leakage concerns for mineralization methods compared to saline storage methods and therefore potentially lower long-term monitoring costs. The costs and benefits of CO2 mineralization are compared to those of CO2 storage in saline reservoirs using estimates of pressure-limited dynamic storage capacity. This report highlights the regional potential of areas in the United States for in situ and ex situ storage, as well as their proximity to potential sources of CO2. Especially suitable targets include asbestos or other ultramafic mine tailings, in situ ultramafic rocks on the East and West Coasts, the Columbia River basalts in the Pacific Northwest, the Midcontinent Rift basalts in the midcontinent, and the basaltic Hawaiian Islands.

Improved automated detection of subpixel-scale inundation – Revised Dynamic Surface Water Extent (DSWE) partial surface water tests

Released February 19, 2019 11:45 EST

2019, Remote Sensing (11) 1-26

John W. Jones

In order to produce useful hydrologic and aquatic habitat data from the Landsat system, the U.S. Geological Survey has developed the “Dynamic Surface Water Extent” (DSWE) Landsat Science Product. DSWE will provide long-term, high-temporal resolution data on variations in inundation extent. The model used to generate DSWE is composed of five decision-rule based tests that do not require scene-based training. To allow its general application, required inputs are limited to the Landsat at-surface reflectance product and a digital elevation model. Unlike other Landsat-based water products, DSWE includes pixels that are only partially covered by water to increase inundation dynamics information content. Previously published DSWE model development included one wetland-focused test developed through visual inspection of field-collected Everglades spectra. A comparison of that test’s output against Everglades Depth Estimation Network (EDEN) in situ data confirmed the expectation that omission errors were a prime source of inaccuracy in vegetated environments. Further evaluation exposed a tendency toward commission error in coniferous forests. Improvements to the subpixel level “partial surface water” (PSW) component of DSWE was the focus of this research. Spectral mixture models were created from a variety of laboratory and image-derived endmembers. Based on the mixture modeling, a more “aggressive” PSW rule improved accuracy in herbaceous wetlands and reduced errors of commission elsewhere, while a second “conservative” test provides an alternative when commission errors must be minimized. Replication of the EDEN-based experiments using the revised PSW tests yielded a statistically significant increase in mean overall agreement (4%, p = 0.01, n = 50) and a statistically significant decrease (11%, p = 0.009, n = 50) in mean errors of omission. Because the developed spectral mixture models included image-derived vegetation endmembers and laboratory spectra for soil groups found across the US, simulations suggest where the revised DSWE PSW tests perform as they do in the Everglades and where they may prove problematic. Visual comparison of DSWE outputs with an unusual variety of coincidently collected images for locations spread throughout the US support conclusions drawn from Everglades quantitative analyses and highlight DSWE PSW component strengths and weaknesses.

Estimating uncertainty of North American landbird population sizes

Released February 19, 2019 11:38 EST

2019, Avian Conservation and Ecology (14)

Jessica C. Stanton, Peter J. Blancher, Kenneth V. Rosenberg, Arvind O. Panjabi, Wayne E. Thogmartin

An important metric for many aspects of species conservation planning and risk assessment is an estimate of total population size. For landbirds breeding in North America, Partners in Flight (PIF) generates global, continental, and regional population size estimates. These estimates are an important component of the PIF species assessment process, but have also been used by others for a range of applications. The PIF population size estimates are primarily calculated using a formula designed to extrapolate bird counts recorded by the North American Breeding Bird Survey (BBS) to regional population estimates. The extrapolation formula includes multiple assumptions and sources of uncertainty, but there were previously no attempts to quantify this uncertainty in the published population size estimates aside from a categorical data quality score. Using a Monte Carlo approach, we propagated the main sources of uncertainty arising from individual components of the model through to the final estimation of landbird population sizes. This approach results in distributions of population size estimates rather than point estimates. We found the width of uncertainty of population size estimates to be generally narrower than the order-of-magnitude distances between the population size score categories PIF uses in the species assessment process, suggesting confidence in the categorical ranking used by PIF. Our approach provides a means to identify species whose uncertainty bounds span more than one categorical rank, which was not previously possible with the data quality scores. Although there is still room for additional improvements to the estimation of avian population sizes and uncertainty, particularly with respect to replacing categorical model components with empirical estimates, our estimates of population size distributions have broader utility to a range of conservation planning and risk assessment activities relying on avian population size estimates.

Potential for increased inundation in flood-prone regions of southeast Florida in response to climate and sea-level changes in Broward County, Florida, 2060–69

Released February 19, 2019 11:28 EST

2019, Scientific Investigations Report 2018-5125

Jeremy D. Decker, Joseph D. Hughes, Eric D. Swain

The U.S. Geological Survey, in cooperation with Broward County Environmental Planning and Resilience Division, has developed county-scale and local-scale groundwater/surface-water models to study the potential for increased inundation and flooding in eastern Broward County that are due to changes in future climate and sea-level rise. These models were constructed by using MODFLOW 2005, with the surface-water system represented by using the Surface-Water Routing process and a new Urban Runoff process. The local-scale model allowed the use of finer grid resolution in a selected area of the county, whereas the county-scale model provided boundary conditions for the local-scale model and insight into the hydrologic behavior of the larger system. The aquifer layering, properties, and boundaries relied heavily on a previous three-dimensional variable-density solute-transport model of the same area developed by the U.S. Geological Survey. The surface-water system within these new models actively simulates a part of the extensive canal network by using level-pool routing and active structure operations within the Surface-Water Routing process. These models were used to simulate a historical base-case period (1990–99) by using measured data and regional climate model rainfall and potential evapotranspiration output. The simulated flow and water-level results generally captured the behavior of the hydrologic system. A future period (2060–69) was simulated by using regional climate model rainfall and potential evapotranspiration output representing a wetter and drier future and low, intermediate, and high sea-level rise projections. The results were used to evaluate the potential effects on the surface-water drainage system, coastal-structure operation, and wet-season groundwater levels.

Future period simulations using the county-scale model indicate that (1) the effects of the changing climate and sea level are much more evident in eastern and coastal areas of Broward County compared to western areas, with increases in groundwater level nearly equivalent to sea-level rise; (2) coastal groundwater-level increases are distributed farther inland in the wetter future scenarios than in the drier future scenarios; (3) water levels at the westernmost groundwater station locations exhibited little change caused by sea-level rise and showed more dependence on changes in precipitation; (4) there was a reduced west-to-east groundwater gradient with increasing sea-level rise; and (5) increased downstream tidal stage at the S–13 structure resulted in increased reliance on the pump to control upstream inland canal stages. Future simulations using the local-scale model indicate similar behavior as seen in the county-scale model: (1) the coastal areas exhibited the largest impacts in groundwater levels in the future scenarios; (2) the westernmost, interior areas exhibited little change during the future scenarios; and (3) there was an increased reliance on the pump at the S–13 coastal structure but to a lesser extent than indicated in the county-scale model because of the reduced temporal scale of the local-scale model.

Possible adaptation and mitigation strategies were simulated to evaluate the county-scale and local-scale models’ ability to simulate hydrologic changes. Alterations to S–13 pump operations within the county-scale model were tested, and results indicate a reduced effect of sea-level rise inland of the control structure, but the affected area is spatially limited. The concept of using pumps to reduce the local groundwater levels in two neighborhood-sized areas was tested by using the local-scale model. The MODFLOW 2005 Drain package was used to remove groundwater by using drainage elevations set to zero, 1 foot, and 2 feet above average wet-season groundwater levels. Area 1 was well connected to coastal boundaries, and a high rate of groundwater removal was required, whereas the rate of groundwater removal required was greatly reduced in Area 2, which is less connected to tidal boundaries. Water for these scenarios was assumed to be pumped to tide with no downstream effects.

Unravelling the complexity of magma plumbing at Mount St. Helens: A new trace element partitioning scheme for amphibole

Released February 19, 2019 11:22 EST

2019, Contributions to Mineralogy and Petrology (174) 1-15

Madeleine C. S. Humphreys, George F. Cooper, Jing Zhang, Matthew W. Loewen, Adam J. R. Kent, Colin G. Macpherson, Jon P. Davidson

Volcanoes at subduction zones reside above complex magma plumbing systems, where individual magmatic components may originate and interact at a range of pressures. Because whole-rock compositions of subduction zone magmas are the integrated result of processes operating throughout the entire plumbing system, processes such as mixing, homogenisation and magma assembly during shallow storage can overprint the chemical signatures of deeper crustal processes. Whereas melt inclusions provide an effective way to study the uppermost 10–15 km of the plumbing system, challenges remain in understanding magma intrusion, fractionation and hybridisation processes in the middle to lower crust (15–30 km depth), which commonly involves amphibole crystallisation. Here, we present new insights into the mid-crustal plumbing system at Mount St. Helens, USA, using multiple regression methods to calculate trace element partition coefficients for amphibole phenocrysts, and thus infer the trace element compositions of their equilibrium melts. The results indicate vertically distributed crystal fractionation, dominated by amphibole at higher pressures and in intermediate melts, and by plagioclase at lower pressures. Variations in Nb, Zr and REE concentrations at intermediate SiO2 contents suggest repeated scavenging of partially remelted intrusive material in the mid-crust, and mixing with material from geochemically diverse sources. Amphibole is an effective probe for deep crustal magmatism worldwide, and this approach offers a new tool to explore the structure and chemistry of arc magmas, including those forming plutonic or cumulate materials that offer no other constraints on melt composition.