Publications recently added to the Pubs Warehouse

(500 records max)

Assessment of Undiscovered Continuous Oil Resources of the East Gobi, Nyalga, Tamtsag-Hailar, Erlian, and Yingen Basins of Mongolia and China, 2018

Released August 15, 2018 14:50 EST

2018, Fact Sheet 2018-3040

Christopher J. Schenk, Tracey J. Mercier, Janet K. Pitman, Thomas M. Finn, Cheryl A. Woodall, Kristen R. Marra, Phuong A. Le, Heidi M. Leathers-Miller

Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean continuous resources of 1.1 billion barrels of oil and 674 billion cubic feet of associated gas in the East Gobi, Nyalga, Tamtsag-Hailar, Erlian, and Yingen basins of Mongolia and China.

Assessment of Undiscovered Conventional Oil Resources of the East Gobi, Nyalga, Tamtsag-Hailar, Erlian, and Yingen Basins of Mongolia and China, 2018

Released August 15, 2018 14:50 EST

2018, Fact Sheet 2018-3041

Christopher J. Schenk, Tracey J. Mercier, Janet K. Pitman, Thomas M. Finn, Cheryl A. Woodall, Kristen R. Marra, Phuong A. Le, Heidi M. Leathers-Miller

Using a geology-based assessment methodology, the U.S. Geological Survey estimated undiscovered, technically recoverable mean conventional resources of 187 million barrels of oil and 85 billion cubic feet of gas in the East Gobi, Nyalga, Tamtsag-Hailar, Erlian, and Yingen basins of Mongolia and China.

Actinorhizal species influence plant and soil nitrogen status of semiarid shrub-dominated ecosystems in the western Great Basin, USA

Released August 15, 2018 14:36 EST

2018, Journal of Arid Environments (157) 48-56

Stephanie M. Freund, Fiona M. Soper, Simon R. Poulson, Paul C. Selmants, Benjamin W. Sullivan

Actinorhizal plants form symbiotic root associations with dinitrogen (N2) fixing Frankia and are abundant in North American cold deserts. However, the extent to which actinorhizal species are actively fixing N2 or altering ecosystem nitrogen (N) availability remains unclear. We used the 15N natural abundance technique to measure how three widespread actinorhizal species in the western Great Basin of western North America acquired N and influenced soil N cycling and the N status of the surrounding non-fixing plant community. We compared foliar and soil N concentrations and δ15N and soil biogeochemistry between reference plots and plots dominated by actinorhizal species. Actinorhizal species may be actively fixing N and influencing the N status of the surrounding ecosystem. Foliar δ15N of actinorhizal shrubs was significantly depleted compared to non-actinorhizal species. Non-actinorhizal plants in the presence of actinorhizal species showed depleted foliar δ15N and higher foliar N concentrations than in reference plots. Rates of N transformations in reference plots were similar to rates in actinorhizal plots; isotopic differences between plot types could not be explained by differences in N loss pathways. Actinorhizal species influence N cycling and availability in N-limited cold deserts, in a manner similar to leguminous plants in warm arid regions.

Science alive and well in North American wildlife management

Released August 15, 2018 14:33 EST

2018, Applied Ecology and Environmental Research

James Nichols, Fred A. Johnson, Byron K. Williams, G. Scott Boomer

Artelle et al. (1) entitled a recent article with the provocative claim: “Hallmarks of science missing from North American wildlife management”. Although we agree with some of the concerns and recommendations of Artelle et al. (1), we believe that the article is misleading about the distinction between science and management, the role of science in wise management, and the degree to which science is used in North American wildlife management. Here we distinguish between science and management, specify an appropriate role of science in management, and document the explicit use of science in at least some programs of North American wildlife management.

Insight into infectious hematopoietic necrosis virus (IHNV) in Chinese rainbow trout aquaculture from virus isolated from 7 provinces in 2010–2014

Released August 15, 2018 14:30 EST

2018, Aquaculture (496) 239-246

Peng Jia, Rachel B. Breyta, Qing Li, Xu Qian, Bing Wu, Wei Zheng, Zhiqing Wen, Ying Liu, Gael Kurath, Qunyi Hua, Ningyi Jin, Hong Liu

The aquatic rhabdovirus infectious hematopoietic necrosis virus (IHNV) currently causes substantial fish losses in Chinese coldwater aquaculture. While IHNV was first reported in China in 1985 and has since undergone considerable spread, little is known about the underlying epidemiological patterns like introduction sources and transmission routes. In this study, we examined epidemiological and phylogenetic data for 50 IHNV isolates from 7 provinces in China detected in 2010–2014 (Liaoning, n = 33; Jilin, n = 3; Heilongjiang, n = 1; Yunnan, n = 2; Sichuan, n = 1; Hebei, n = 5; Gansu, n = 5). Features of case details include highest mortality associated with water temperatures of 8–10 °C and symptomatic disease observed in adult rainbow trout. Sequence comparisons of the midG sequences of 50 strains revealed 11 different sequence types. One sequence type, mG801J, was predominantly detected, being found in 38 of 50 isolates. Phylogenetic analyses of the new midG sequence types showed that 49 of 50 IHNV isolates are closely related to one another and all descend from the previously described J Nagano subgroup, forming the monophyletic group J Nagano-China clade. This indicates that the majority of IHNV circulating within China is descended from a single importation event from elsewhere in Asia. The one observed exception was the detection of a novel genotype belonging to the previously described MN subgroup. This genotype was identified in Liaoning province, and indicates a second introduction event, one that does not appear to have resulted in diversification and spread. These results indicate that continued surveillance of IHNV in China is necessary to understand and manage viral transmission dynamics within China over time.

Responses of hatchery‐ and natural‐origin adult spring Chinook Salmon to a trap‐and‐haul reintroduction program

Released August 15, 2018 14:26 EST

2018, North American Journal of Fisheries Management

Tobias J. Kock, Russell W. Perry, Adam C. Pope, John D. Serl, Mike Kohn, Theresa L. Liedtke

The construction of impassable dams severely affected many Pacific salmon Oncorhynchus spp. populations, resulting in reintroduction efforts that are now focused on returning anadromous fish to areas located upstream of these dams. A primary strategy for moving adult salmon and steelhead O. mykiss around a dam or multiple dams involves trapping fish downstream and transporting them to upstream areas (“trap and haul”) for spawning. We conducted a 4‐year radiotelemetry study to evaluate behavior and movement patterns of hatchery‐ and natural‐origin adult spring Chinook Salmon O. tshawytscha after a trap‐and‐haul program was implemented around three dams on the Cowlitz River, Washington. A multistate model was used to describe how factors such as origin, sex, release site location, and discharge affected transition rates to riverine areas where spawning habitat was located. Natural‐origin Chinook Salmon moved upstream from a reservoir release site and entered one of two rivers more quickly and in greater proportions than hatchery‐origin fish. Results from the multistate model indicated that transition rates from the reservoir to the Cowlitz River were 2.2 times higher for natural‐origin Chinook Salmon than for hatchery‐origin fish. About one‐half (49.6%) of the reservoir‐released hatchery‐origin Chinook Salmon moved upstream into the Cowlitz River or the Cispus River during the spawning period. The release of hatchery‐origin Chinook Salmon directly into these rivers increased the percentage of fish with river fates during the spawning period to 72.3–75.4%. Results from the multistate model showed that factors such as release site location, origin, day of year, and discharge were important predictors of transition intensities between specific locations in the study area. These findings illustrate the need to evaluate how salmon and steelhead respond to trap‐and‐haul methods, allowing for better management of reintroduction efforts in the future.

Flyway structure in the circumpolar greater white‐fronted goose

Released August 15, 2018 14:08 EST

2018, Ecology and Evolution

Robert E. Wilson, Craig R. Ely, Sandra L. Talbot

Dispersal and migratory behavior are influential factors in determining how genetic diversity is distributed across the landscape. In migratory species, genetic structure can be promoted via several mechanisms including fidelity to distinct migratory routes. Particularly within North America, waterfowl management units have been delineated according to distinct longitudinal migratory flyways supported by banding data and other direct evidence. The greater white‐fronted goose (Anser albifrons) is a migratory waterfowl species with a largely circumpolar distribution consisting of up to six subspecies roughly corresponding to phenotypic variation. We examined the rangewide population genetic structure of greater white‐fronted geese using mtDNA control region sequence data and microsatellite loci from 23 locales across North America and Eurasia. We found significant differentiation in mtDNA between sampling locales with flyway delineation explaining a significant portion of the observed genetic variation (~12%). This is concordant with band recovery data which shows little interflyway or intercontinental movements. However, microsatellite loci revealed little genetic structure suggesting a panmictic population across most of the Arctic. As with many high‐latitude species, Beringia appears to have played a role in the diversification of this species. A common Beringian origin of North America and Asian populations and a recent divergence could at least partly explain the general lack of structure at nuclear markers. Further, our results do not provide strong support for the various taxonomic proposals for this species except for supporting the distinctness of two isolated breeding populations within Cook Inlet, Alaska (A. a. elgasi) and Greenland (A. a. flavirostris), consistent with their subspecies status.

A transcriptome resource for the Arctic Cod (Boreogadus saida)

Released August 15, 2018 14:00 EST

2018, Marine Genomics

Robert E. Wilson, Damian M. Menning, Kate Wedemeyer, Sandra L. Talbot

Arctic Cod (Boreogadus saida) serve as an important link in Arctic food webs and are thus considered an important species for environmental monitoring. RNA-Seq was conducted on samples from wild-collected individuals representing various age classes and tissue types to obtain as complete a transcriptome as possible on an Illumina MiSeq, which resulted in a total of 64,457 transcripts with an average length of 295 bp. We identified well-known genes that are associated with temperature change or response to pollutants. This RNA-Seq effort provides the first insight into the B. saida transcriptome, which can be a starting point for investigations identifying genes for local adaptation and genomic responses to future environmental change.

Evaluating the waterfowl breeding population and habitat survey for scaup

Released August 15, 2018 13:42 EST

2018, Journal of Wildlife Management (82) 1252-1262

Michael L. Schummer, Alan D. Afton, Shannon S. Badzinski, Scott A. Petrie, Glenn H. Olsen, Mark A. Mitchell

Potential bias in breeding population estimates of certain duck species from the Waterfowl Breeding Population and Habitat Survey (WBPHS) has been a concern for decades. The WBPHS does not differentiate between lesser (Aythya affinis) and greater (Amarila) scaup, but lesser scaup comprise 89% of the combined scaup population and their population estimates are suspected to be biased. We marked female lesser scaup (i.e., marked scaup) in the Mississippi and Atlantic Flyways, Canada and United States, with implantable satellite transmitters to track their spring migration through the traditional and eastern survey areas of the WBPHS, 2005–2010. Our goal was to use data independent of the WBPHS to evaluate whether breeding population estimates for scaup were biased and identify variables that might be used in the future to refine population estimates. We found that the WBPHS estimates of breeding scaup are biased because, across years, only 30% of our marked scaup had settled for the breeding period when the strata in which they settled were surveyed, 43% were available to be counted in multiple survey strata as their migration continued during the WBPHS, 32% settled outside the WBPHS area, the number of times a marked scaup was available to be counted by survey crews varied positively with the latitude that a marked scaup settled on breeding areas, the probability of a marked scaup being in a stratum while it was surveyed varied among years, and these probabilities were positively correlated with the traditional and eastern breeding population estimates for scaup. Annual population estimates derived from banding data provide a less biased and preferable method of monitoring scaup population status and trend. Development of models that include metrics such as survey stratum latitude and annual spring environmental conditions might potentially be used to improve scaup breeding population estimates derived from the WBPHS, but independent estimates from banding data would be important to evaluate such models.

Status of Groundwater-Level Altitudes and Long-term Groundwater-Level Changes in the Chicot, Evangeline, and Jasper Aquifers, Houston-Galveston Region, Texas, 2018

Released August 15, 2018 13:11 EST

2018, Scientific Investigations Report 2018-5101

Sachin D. Shah, Jason K. Ramage, Christopher L. Braun

Since the early 1900s, most of the groundwater withdrawals in the Houston-Galveston region, Texas, have been from the three primary aquifers that compose the Gulf Coast aquifer system—the Chicot, Evangeline, and Jasper aquifers. Withdrawals from these aquifers are used for municipal supply, industrial, and irrigation purposes. This report, prepared by the U.S. Geological Survey in cooperation with the Harris-Galveston Subsidence District, City of Houston, Fort Bend Subsidence District, Lone Star Groundwater Conservation District, and Brazoria County Groundwater Conservation District, is one in an annual series of reports depicting the status of groundwater-level altitudes and long-term groundwater-level changes in the Chicot, Evangeline, and Jasper aquifers in the Houston-Galveston region. This report contains regional-scale maps depicting approximate 2018 groundwater-level altitudes (represented by measurements made during December 2017 through March 2018) and long-term groundwater-level changes for the Chicot, Evangeline, and Jasper aquifers.

In 2018, groundwater-level-altitude contours for the Chicot aquifer ranged from 200 feet (ft) below the North American Vertical Datum of 1988 (hereinafter referred to as “datum”) to 200 ft above datum. The 1977–2018 groundwater-level-change contours for the Chicot aquifer depict a large area of decline in groundwater-level altitudes (120 ft) in northwestern Harris County. The largest rise in groundwater-level altitudes in the Chicot aquifer from 1977 to 2018 (180 ft) was in southeastern Harris County.

Groundwater-level-altitude contours for the Evangeline aquifer ranged from 250 ft below datum to 200 ft above datum in 2018. The 1977–2018 groundwater-level-change contours for the Evangeline aquifer depict broad areas where groundwater-level altitudes either declined or rose. The largest decline in groundwater-level altitudes (320 ft) was in southern Montgomery County. The largest rise in groundwater-level altitudes in the Evangeline aquifer from 1977 to 2018 (240 ft) was in southeastern Harris County.

In 2018, groundwater-level-altitude contours for the Jasper aquifer ranged from 200 ft below datum to 200 ft above datum. The 2000–18 groundwater-level-change contours for the Jasper aquifer depict groundwater-level declines throughout most of the study area where groundwater-level-altitude data from the Jasper aquifer were collected, with the largest decline (200 ft) in southern Montgomery County.

An Individual-Based Model for Predicting Dynamics of a Newly Established Mexican Wolf (Canis lupus baileyi) Population—Final Report

Released August 15, 2018 12:26 EST

2018, Open-File Report 2018-1126

Jay V. Gedir, James W. Cain

Project Summary

The Mexican wolf recovery team proposed to establish other populations of Mexican wolves (Canis lupus baileyi) in the Southwest (U.S. Fish and Wildlife Service, 1982). We were tasked to conduct an extensive simulation modeling exercise to determine release strategies (in conjunction with management actions) that best predict establishment of a new Mexican wolf population. Our objectives were to determine optimal release and management strategies for population establishment and growth. This is a retrospective analysis utilizing data from 1998 to 2014, and during this period, we divided management strategies into two phases; (1) 1998–2008, where nuisance wolves (i.e., wolves that exhibit nuisance behavior or depredate livestock) were managed primarily through lethal removals and removals to captivity, and (2) 2009–2014, when lethal removals ceased and diversionary feeding was provided to denning packs to dissuade wolves from conflict with humans. Management strategies from the second phase are being used for management of the current Mexican wolf population, and demographic rates derived from alternate population modeling in Vortex incorporating post-2008 wolf data are being used to guide future recovery efforts. Therefore, demographic rates estimated from our retrospective analysis will differ (i.e., due to our unique approach to the analyses and the demographic rates being derived from a different dataset), and are intended solely to address the objectives of this report, and are not intended as basis for the development of management recommendations for the current Mexican wolf population. Using individual-based models, we tested dozens of scenarios and derived an optimal release strategy that had the highest probability of establishing a new population and which maximized subsequent post-release growth, and in this report, we present these model results. Findings from this research will improve our understanding of release strategies that yield growing populations, advance our understanding of the demands of reintroducing large carnivores, and provide insight into beneficial strategies that could aid other species reintroduction programs.

Landsat collections

Released August 15, 2018 00:00 EST

2018, Fact Sheet 2018-3049

Michelle Knuppe

In 2016, the U.S. Geological Survey reorganized the Landsat archive into a tiered collection structure, which ensures that Landsat Level-1 products provide a consistent archive of known data quality to support time-series analyses and data “stacking” while controlling continuous improvement of the archive and access to all data as they are acquired. Landsat Collection 1 required the reprocessing of all archived Landsat data to achieve radiometric and geometric consistency of Level-1 products through time and across all Landsat sensors. 

Estimating distemper virus dynamics among wolves and grizzly bears using serology and Bayesian state‐space models

Released August 14, 2018 14:12 EST

2018, Ecology and Evolution

Paul C. Cross, Frank T. van Manen, Mafalda Viana, Emily S. Almberg, Daniel Bachen, Ellen E. Brandell, Mark A. Haroldson, Peter J. Hudson, Daniel R. Stahler, Douglas W. Smith

Many parasites infect multiple hosts, but estimating the transmission across host species remains a key challenge in disease ecology. We investigated the within and across host species dynamics of canine distemper virus (CDV) in grizzly bears (Ursus arctos) and wolves (Canis lupus) of the Greater Yellowstone Ecosystem (GYE). We hypothesized that grizzly bears may be more likely to be exposed to CDV during outbreaks in the wolf population because grizzly bears often displace wolves while scavenging carcasses. We used serological data collected from 1984 to 2014 in conjunction with Bayesian state‐space models to infer the temporal dynamics of CDV. These models accounted for the unknown timing of pathogen exposure, and we assessed how different testing thresholds and the potential for testing errors affected our conclusions. We identified three main CDV outbreaks (1999, 2005, and 2008) in wolves, which were more obvious when we used higher diagnostic thresholds to qualify as seropositive. There was some evidence for increased exposure rates in grizzly bears in 2005, but the magnitude of the wolf effect on bear exposures was poorly estimated and depended upon our prior distributions. Grizzly bears were exposed to CDV prior to wolf reintroduction and during time periods outside of known wolf outbreaks, thus wolves are only one of several potential routes for grizzly bear exposures. Our modeling approach accounts for several of the shortcomings of serological data and is applicable to many wildlife disease systems, but is most informative when testing intervals are short. CDV circulates in a wide range of carnivore species, but it remains unclear whether the disease persists locally within the GYE carnivore community or is periodically reintroduced from distant regions with larger host populations.

Moving from generalisations to specificity about mangrove-saltmarsh dynamics

Released August 14, 2018 13:58 EST

2018, Wetlands

Kerrylee Rogers, Ken W. Krauss

Spatial and temporal variability in factors influencing mangrove establishment and survival affects the distribution of mangrove, particularly near their latitudinal limit, where mangrove expansion into saltmarsh is conspicuous. In this paper the spatial variability in mangrove distribution and variability in factors influencing mangrove establishment and survival during the Quaternary period are reviewed, focussing on research at latitudinal limits in Australia and mainland USA. Despite similarities in the response of mangrove to some drivers, the expression of these drivers is both spatially and temporally variable, demonstrating the need for analyses of mangrove-saltmarsh dynamics to move beyond generalisations and incorporate regional and local-scale specificity. We propose i) that precursory recognition that ‘correlation does not mean causation’ is inadequate and assumptions, caveats, and limitations should be clearly articulated in correlative studies; ii) experimental design in manipulative experiments must also articulate the spatial and temporal scale to which the analysis is relevant; and iii) analyses that draw from a range of methods will provide greater confidence. Integrated research programs that transect spatial and temporal scales and incorporate a range of techniques are essential to improve projections. Mangrove-saltmarsh distribution research should move beyond simple models that assume equilibrium between realised and fundamental niches.

Flushing of the deep Pacific Ocean and the deglacial rise of atmospheric CO2 concentrations

Released August 14, 2018 13:56 EST

2018, Nature Geoscience

Jianghui Du, Brian Haley, Alan Mix, Maureen Walczak, Summer K. Praetorius

During the last deglaciation (19,000–9,000 years ago), atmospheric CO2increased by about 80 ppm. Understanding the mechanisms responsible for this change is a central theme of palaeoclimatology, relevant for predicting future CO2 transfers in a warming world. Deglacial CO2 rise hypothetically tapped an accumulated deep Pacific carbon reservoir, but the processes remain elusive as they are underconstrained by existing tracers. Here we report high-resolution authigenic neodymium isotope data in North Pacific sediment cores and infer abyssal Pacific overturning weaker than today during the Last Glacial Maximum but intermittently stronger during steps of deglacial CO2 rise. Radiocarbon evidence suggestive of relatively ‘old’ deglacial deep Pacific water is reinterpreted here as an increase in preformed 14C age of subsurface waters sourced near Antarctica, consistent with movement of aged carbon out of the deep ocean and release of CO2 to the atmosphere during the abyssal flushing events. The timing of neodymium isotope changes suggests that deglacial acceleration of Pacific abyssal circulation tracked Southern Hemisphere warming, sea-ice retreat and increase of mean ocean temperature. The inferred magnitude of circulation changes is consistent with deep Pacific flushing as a significant, and perhaps dominant, control of the deglacial rise of atmospheric CO2.

Global and Arctic climate sensitivity enhanced by changes in North Pacific heat flux

Released August 14, 2018 13:54 EST

2018, Nature Communications (9) 1-12

Summer K. Praetorius, Maria A. Rugenstein, Geeta Persad, Ken Caldeira

Arctic amplification is a consequence of surface albedo, cloud, and temperature feedbacks, as well as poleward oceanic and atmospheric heat transport. However, the relative impact of changes in sea surface temperature (SST) patterns and ocean heat flux sourced from different regions on Arctic temperatures are not well constrained. We modify ocean-to-atmosphere heat fluxes in the North Pacific and North Atlantic in a climate model to determine the sensitivity of Arctic temperatures to zonal heterogeneities in northern hemisphere SST patterns. Both positive and negative ocean heat flux perturbations from the North Pacific result in greater global and Arctic surface air temperature anomalies than equivalent magnitude perturbations from the North Atlantic; a response we primarily attribute to greater moisture flux from the subpolar extratropics to Arctic. Enhanced poleward latent heat and moisture transport drive sea-ice retreat and low-cloud formation in the Arctic, amplifying Arctic surface warming through the ice-albedo feedback and infrared warming effect of low clouds. Our results imply that global climate sensitivity may be dependent on patterns of ocean heat flux in the northern hemisphere.

Spatial relationships of levees and wetland systems within floodplains of the Wabash Basin, USA

Released August 14, 2018 13:40 EST

2018, Journal of the American Water Resources Association (54) 934-948

Ryan R. Morrison, Erin N. Bray, Fernando Nardi, Antonio Annis, Quan Dong

Given the unique biogeochemical, physical, and hydrologic services provided by floodplain wetlands, proper management of river systems should include an understanding of how floodplain modifications influence wetland ecosystems. The construction of levees can reduce river–floodplain connectivity, yet it is unclear how levees affect wetlands within floodplains, let alone the cumulative impacts within an entire watershed. This paper explores spatial relationships between levee and floodplain wetland systems in the Wabash Basin, United States. We used a hydrogeomorphic floodplain delineation technique to map floodplain extents and identify wetlands that may be hydrologically connected to river networks. We then spatially examined the relationship between levee presence, wetland area, and other river network attributes within discrete subbasins. Our results show that cumulative wetland area is relatively constant in subbasins that contain levees, regardless of maximum stream order within the subbasin. In subbasins that do not contain levees, cumulative wetland area increases with maximum stream order. However, we found that wetland distributions around levees can be complex, and further studies on the influence of levees on wetland habitat may need to consider finer resolution spatial scales.

Probabilistic models of seafloor composition using multispectral acoustic backscatter: The benthic detectorists

Released August 13, 2018 16:06 EST

2018, Conference Paper

Daniel Buscombe, Paul E. Grams, Matthew Kaplinski

We describe and compare two probabilistic models for task-specific seafloor characterization based on multispectral backscatter. We examine whether generative or discriminative approaches to supervised seafloor characterization do better at harnessing the greatly increased information about seafloor substrate composition that is encoded in the backscattering response across multiple frequencies. A Gaussian mixture model (GMM) is proposed as a generative model, and a fully-connected conditional random field (CRF) is proposed as a discriminative model. Either model uses input data derived from monospectral or multispectral backscatter without modification. The CRF approach considers both the relative backscatter magnitudes of different substrates as well as their relative proximity, and can be optimized using parameters. The GMM model, in contrast, includes no spatial information in its estimates, being based solely on relative backscatter magnitudes. Both GMM and CRF modeling approaches perform better with multispectral backscatter compared to monospectral, significantly outperforming all three monospectral frequencies. With multispectral backscatter inputs, based on average classification accuracies alone, there was little to choose between the two modeling approaches (classification accuracy of 81% and 83% for GMM and CRF models, respectively, evaluated using 50% of available bed observations to train and 50% to test the models). However, a CRF model that has been optimized with respect to its tunable parameters tends to produce higher posterior probabilities (i.e. greater certainty) for its classifications. Using monospectral backscatter inputs, the CRF model significantly outperformed the GMM model in terms of average classification accuracy. On balance, therefore, based on the evidence presented here, the CRF is suggested to be the superior approach for task-specific seafloor classification. Although further work using additional data is required to further examine this conclusion, the work presented here will guide and focus subsequent research efforts as more areas of the seafloor are mapped with the new technology. In order to facilitate these efforts, the algorithms presented here are encoded in a freely available python toolbox for Probabilistic acoustic Sediment Mapping, called PriSM , that can be used for both monospectral and multispectral backscatter. Finally, we show that application of the CRF model to the outputs of a geoacoustical model of seafloor scattering results in realistic substrate classification boundaries. This hybrid CRF and physics-based approach can predict the physical properties of the seafloor at a finer spatial resolution than is possible using the geoacoustical model alone.

Promoting synergy in the innovative use of environmental data—Workshop summary

Released August 13, 2018 14:30 EST

2018, Open-File Report 2018-1104

Healy Hamilton, Gerald F. Guala, Annie Simpson

From December 2 to 4, 2015, NatureServe and the U.S. Geological Survey organized and hosted a biodiversity and ecological informatics workshop at the U.S. Department of the Interior in Washington, D.C. The workshop objective was to identify user-driven future directions and areas of collaboration in advanced applications of environmental data applied to forecasting and decision making for the sustainability of biodiversity and ecosystem services. Substantial effort to recruit attendees from diverse Federal, State, and private sector organizations successfully attracted participants from 20 Federal agencies and 48 different institutions in the academic, nonprofit, State government, and commercial sectors; the total number of attendees ranged from 100 to 144 during the 3-day workshop. The first one-half of the workshop was divided into 7 plenary sessions and 3 sets of lightening talk sessions organized by sector, providing 48 oral and visual plenary presentations that shared diverse perspectives on biodiversity and ecological informatics, including original biospatial analyses from 6 graduate student map contest winners. The second one-half of the workshop focused on 10 breakout sessions with participant-driven themes from the environmental data sphere and concluded with an address by the Director of the U.S. Fish and Wildlife Service. The workshop was structured to encourage interactivity. About 80–90 percent of attendees provided direct feedback using clicker devices for specific questions related to biodiversity and ecological data uses and needs, and 10 breakout session leaders shared the highlights of their group discussions during the final workshop plenary sessions. Participants were encouraged to use the Twitter hashtag #ShareUrData. Over lunch on day 2 there were 20 simultaneous presentations of tools and apps during a special “Tools Café” session.

The 10 participant-defined breakout session topics are listed below:

Numerous common themes that emerged from the workshop include the following:

Herbicides and herbivory interact to drive plant community and crop‐tree establishment

Released August 13, 2018 13:50 EST

2018, Ecological Applications

Thomas D. Stokely, Jake Verschuyl, Joan Hagar, Matthew G. Betts

Land management practices often directly alter vegetation structure and composition, but the degree to which ecological processes such as herbivory interact with management to influence biodiversity is less well understood. We hypothesized that large herbivores compound the effects of intensive forest management on early seral plant communities and plantation establishment (i.e., tree survival and growth), and the degree of such effects is dependent on the intensity of management practices. We established 225 m2 wild‐ungulate (deer and elk) exclosures, nested within a manipulated gradient of management intensity (no‐herbicide Control, Light herbicide, Moderate herbicide and Intensive herbicide treatments), replicated at the scale of whole harvest units (10‐19 ha). Vegetation structure, composition and crop‐tree responses to herbivory varied across the gradient of herbicide application during the first two years of stand establishment, with herbivory effects most evident at intermediate herbicide treatments. In the Moderate herbicide treatment – which approximates treatments applied to > 2.5 million hectares in Pacific Northwest U.S.A. – foraging by deer and elk resulted in simplified, low‐cover plant communities more closely resembling the Intensive herbicide treatment. Herbivory further suppressed the growth of competing vegetation in the Light herbicide treatment, improving crop‐tree survival, and providing early evidence of an ecosystem service. By changing community composition and vegetation structure, intensive forest management alters foraging selectivity and subsequent plant‐herbivore interactions; initial shifts in early seral communities are likely to influence understory plant communities and tree growth in later stages of forest development.

Biological and ecological science for Ohio—The Buckeye State

Released August 10, 2018 11:56 EST

2018, Fact Sheet 2018-3034

U.S. Geological Survey

Ohio is home to lakes, rivers, streams, wetlands, forests, prairies, and 312 miles of Lake Erie shoreline. These resources sustain Ohio’s communities by supporting vital sectors of the economy and cultural heritage such as fishing, hunting, and other outdoor recreation. Lake Erie provides drinking water for 3 million Ohioans, supports 124,000 Ohio jobs, and generates \$1.8 billion in tourism revenue to the State. Outdoor recreation is enjoyed by nearly 60 percent of Ohio residents. Annually, it is estimated that outdoor recreation generates \$24.3 billion in consumer spending across the State, creates 215,000 jobs, and raises \$1.5 billion in State and local tax revenue.

Macrobenthic infaunal communities associated with deep‐sea hydrocarbon seeps in the northern Gulf of Mexico

Released August 10, 2018 11:40 EST

2018, Marine Ecology

Travis W. Washburn, Amanda W.J. Demopoulos, Paul A. Montagna

There are thousands of seeps in the deep ocean worldwide; however, many questions remain about their contributions to global biodiversity and the surrounding deep‐sea environment. In addition to being globally distributed, seeps provide several benefits to humans such as unique habitats, organisms with novel genes, and carbon regulation. The purpose of this study is to determine whether there are unique seep macrobenthic assemblages, by comparing seep and nonseep environments, different seep habitats, and seeps at different depths and locations. Infaunal community composition, diversity, and abundance were examined between seep and nonseep background environments and among three seep habitats (i.e., microbial mats, tubeworms, and soft‐bottom seeps). Abundances were higher at seep sites compared to background areas. Abundance and diversity also differed among microbial mat, tubeworm, and soft‐bottom seep habitats. Although seeps contained different macrobenthic assemblages than nonseep areas, infaunal communities were also generally unique for each seep. Variability was 75% greater within communities near seeps compared to communities in background areas. Thus, high variability in community structure characterized seep communities rather than specific taxa. The lack of similarity among seep sites supports the idea that there are no specific infauna that can be used as indicators of seepage throughout the northern Gulf of Mexico, at least at higher taxonomic levels.

State-level freshwater mussel programs: Current status and a research framework to aid in mussel management and conservation

Released August 10, 2018 11:36 EST

2018, Fisheries (43) 345-360

Kristen Bouska, Amanda E. Rosenberger, Stephen E. McMurray, Garth A. Lindner, Kayla N. Key

Despite increased focus on their ecology and conservation, freshwater mussels remain one of the most imperiled groups of aquatic organisms. We documented current management actions, resources, and challenges in managing freshwater mussels in the United States through a survey of state natural resource agencies. Approximately 85% of surveyed states (= 40) actively managed mussel populations. Common challenges to mussel conservation included limited funding, lack of public awareness, and poor understanding of habitat needs and risks. We present a research framework, currently underway in Missouri, to support a regional mussel conservation assessment whereby habitat needs are identified, risks are assessed, and standardized protocols are developed to monitor and detect trends in mussel assemblages and threats. The research framework conforms to the National Strategy for the Conservation of Native Freshwater Mollusks and is adaptable to other states. With full consideration of resource limitations, we explore how this framework can improve the effectiveness of mussel conservation efforts.

Classifying physiographic regimes on terrain and hydrologic factors for adaptive generalization of stream networks

Released August 10, 2018 11:31 EST

2018, International Journal of Cartography

Larry V. Stanislawski, Michael P. Finn, Barbara P. Buttenfield

Automated generalization software must accommodate multi-scale representations of hydrographic networks across a variety of geographic landscapes, because scale-related hydrography differences are known to vary in different physical conditions. While generalization algorithms have been tailored to specific regions and landscape conditions by several researchers in recent years, the selection and characterization of regional conditions have not been formally defined nor statistically validated. This paper undertakes a systematic classification of landscape types in the conterminous United States to spatially subset the country into workable units, in preparation for systematic tailoring of generalization workflows that preserve hydrographic characteristics. The classification is based upon elevation, standard deviation of elevation, slope, runoff, drainage and bedrock density, soil and bedrock permeability, area of inland surface water, infiltration-excess of overland flow, and a base flow index. A seven class solution shows low misclassification rates except in areas of high landscape diversity such as the Appalachians, Rocky Mountains, and Western coastal regions.

Stream‐centric methods for determining groundwater contributions in karst mountain watersheds

Released August 10, 2018 11:28 EST

2018, Water Resources Research

Bethany Neilson, Hyrum Tennant, Michelle Barnes, Trinity Stout, Matthew P. Miller, Rachel S. Gabor, Yusef Jameel, Mallory Millington, Andrew Gelderloos, Gabriel J. Bowen, Paul D. Brooks

Climate change influences on mountain hydrology are uncertain, but likely to be mediated through changes in subsurface hydrologic residence times and flowpaths. The heterogeneity of karst aquifers add complexity in assessing the resiliency of these water sources to perturbation, suggesting a clear need to quantify contributions from and losses to these aquifers. Here we develop a stream centric method that combines mass and flow balances to quantify net and gross gains and losses at different spatial scales. We then extend these methods to differentiate between karst conduit and matrix contributions from the aquifer. In the Logan River watershed in Northern Utah we found significant amounts of the river water repeatedly gained and then lost through a 35 km study reach. Further, the direction and amount of water exchanged varied over space, time, and discharge. Streamflow was dominated by discharge of karst conduit groundwater after runoff with increasing, yet still small, fractions of matrix water later in the summer. These findings were combined with geologic information, prior subsurface dye tracing, and chemical sampling to provide additional lines of evidence that repeated groundwater exchanges are likely occurring and river flows are highly dependent on karst aquifer recharge and discharge. Given the large population dependent on karst aquifers throughout the world, there is a continued need to develop simple methods, like those presented here, for determining the resiliency of karst groundwater resources.

Effect of spatial and temporal scale on simulated groundwater recharge investigations

Released August 10, 2018 11:21 EST

2018, Advances in Water Resources (119) 257-270

Fred Tillman, Tom Pruitt, Subhrendu Gangopadhyay

Hydrologic model input datasets such as climate, land use, elevation, soil, and geology information are available in a range of scales for use in water resources investigations. Smaller spatial and temporal scale input data allow groundwater recharge models to simulate more physically realistic processes and presumably result in more accurate estimates of groundwater recharge. Projected climate data are, therefore, often downscaled to smaller spatial and temporal scales for use in these models. It is unknown, however, if increasingly smaller-scale climate data produce substantially different simulated recharge results, either in magnitude or trend. Also, even if simulated recharge results are different at a higher space and time resolution, simulation at coarser resolution might be adequate to provide recharge information at decision scales (e.g., meeting Colorado River compact requirements on a ten-year moving average basis). Historical climate datasets at three spatial (∼800 m, ∼4 km, and ∼12 km) and two temporal (daily and monthly) scales were used in a Soil Water Balance (SWB) model of the upper Colorado River basin (UCRB) to simulate groundwater recharge over the water-year 1982–2014 time period. The magnitude of annual and moving ten-year annual average recharge results for daily climate data were within 5% and 7% of ∼4 km results for ∼800 m and ∼12 km climate data, respectively, with deviations from 1982 to 2014 means within 1% and 3% (median), respectively. Comparison of simulated recharge results using the coarsest spatial and temporal climate data with results from the finest scale data indicated similar small differences over ten-year moving annual averages, over water years, and during high recharge months. While differences in simulated groundwater recharge magnitude, which may be important for groundwater-flow simulations, were substantial during some seasonal comparisons, trends in recharge were almost identical across scales, leading to similar conclusions about change from “normal”. Considering the uncertainty inherent in projected climate data, coarser spatial and longer temporal scale input data may be sufficient for water resources managers who need to understand changes in trends in groundwater recharge over water-year or longer time periods.

Mercury methylation and bioaccumulation in Sinclair Inlet, Kitsap County, Washington

Released August 09, 2018 14:30 EST

2018, Scientific Investigations Report 2018-5063

A.J. Paulson, M.C. Marvin-DiPasquale, P.W. Moran, J.F. DeWild, J.F. Stewart, J. Toft, J.L. Agee, E. Kakouros, L.H. Kieu, B. Carter, R.W. Sheibley, J. Cordell, D. P. Krabbenhoft

The U.S. Geological Survey evaluated the transformation of mercury to bioavailable methylmercury in Sinclair Inlet, Kitsap County, Washington, and assessed the effect of the transformation processes on the mercury burden in marine organisms and sediment. In August 2008, samples of sediment, water, and biota from six sites in Sinclair Inlet and three bays representative of Puget Sound embayments were collected. The extensive sediment sampling included analysis of methylmercury in sediment and porewater, estimates of methylation production potential, and analyses of ancillary constituents associated with organic carbon and reduction-oxidation (redox) conditions to assist in interpreting the mercury results. Analyses of methylmercury in water overlying incubated cores provided an estimate of the release of methylmercury to the water column. Collection of samples for mercury species in the aqueous, particulate (suspended solids), and biological phases, and for ancillary carbon and nitrogen constituents in surface water, continued, on about a monthly schedule, at four stations through August 2009. In February, June, and August 2009, seasonal sediment samples were collected at 20 stations distributed between greater Sinclair Inlet and Operable Unit B Marine of the Bremerton naval complex, Bremerton, Washington, to examine geographical and seasonal patterns of mercury biogeochemistry of sediment in Sinclair Inlet. At six of these seasonal sediment stations, porewater was collected and triplicate core incubation experiments were done.

Median sediment-methylmercury concentrations were not statistically different between the representative bays and Sinclair Inlet. The percentage of sediment methylmercury (relative to total mercury) was actually lower in the Sinclair Inlet sites compared with the representative bays, reflecting the higher sediment total mercury concentration for the Sinclair Inlet stations compared with the representative bays. Likewise, median sediment methylmercury concentrations were not statistically different between the greater Sinclair Inlet stations and the Bremerton naval complex stations; whereas the percentage of sediment methylmercury to total mercury was lower in the Bremerton naval complex due to higher sediment total mercury concentrations than the greater Sinclair Inlet stations. The biogeochemical characteristics of each station, measured by redox, organic carbon, and the seasonal availability of nutrients controlled methylmercury biogeochemistry. Mercury methylation production potential was a function of temperature, concentration of total mercury in sediment, and the percentage of ferrous iron (relative to total measured iron) across all sites. Methylmercury porewater concentrations were best described by using concentrations of dissolved organic carbon and reduction-oxidation conditions. Likewise, the variable fluxes of methylmercury from incubated cores were best described using dissolved organic carbon and reduction-oxidation conditions.

Sinclair Inlet exhibited the classic Puget Sound biological cycle, with spring and autumn phytoplankton blooms resulting in depletion of nitrate, orthophosphate, and silicate in the surface water. Although variable in timing between 2008 and 2009, a strong corresponding seasonal trend of increased availability, incorporation, and bioaccumulation of methylmercury into the food web of Sinclair Inlet occurred during the early spring and summer growing season.

Assessment of undiscovered continuous oil and gas resources in the Upper Cretaceous Tuscaloosa marine shale of the U.S. Gulf Coast, 2018

Released August 09, 2018 13:20 EST

2018, Fact Sheet 2018-3043

Paul C. Hackley, Catherine B. Enomoto, Brett J. Valentine, William A. Rouse, Celeste D. Lohr, Frank T. Dulong, Javin Hatcherian, Sean T. Brennan, William H. Craddock, Thomas M. Finn, Stephanie B. Gaswirth, Phuong A. Le, Heidi M. Leathers-Miller, Kristen R. Marra, Tracey J. Mercier, Stanley T. Paxton, Katherine J. Whidden, Cheryl A. Woodall, Christopher J. Schenk

Using a geology-based assessment methodology, the U.S. Geological Survey assessed mean undiscovered, technically recoverable continuous
resources of 1.5 billion barrels of oil and 4.6 trillion cubic feet of gas in the Upper Cretaceous Tuscaloosa marine shale in onshore and State waters of
Louisiana, Mississippi, Alabama, and Florida in the U.S. Gulf Coast region.

Prepublication communication of research results

Released August 09, 2018 10:24 EST

2018, EcoHealth

Michael J. Adams, Reid N. Harris, Evan H. Campbell Grant, Matthew J. Gray, M. Camille Hopkins, Samuel A. Iverson, Robert Likens, Mark Mandica, Deanna H. Olson, Alex Shepack, Hardin Waddle

Publishing of scientific findings is central to the scientific process, and it is traditional to consider findings “provisional” until accepted by a peer-reviewed journal. Until publication, communication of provisional findings beyond participants in the study is typically limited. This practice helps assure scientific integrity. However, a dilemma arises when a provisional finding has urgent societal consequences that may be exacerbated by delay. This dilemma may be particularly pronounced when a discovery concerns wildlife health, which could have implications for conservation, public health (i.e., zoonoses), or domestic animal health (e.g., avian influenza). A scientist may see a need for prepublication communication but consider such communication to be problematic. We suggest that common concerns about directed prepublication communication are generally misplaced. Our perspective comes from natural resources science and management, but we suspect that this situation could arise in any branch of science and that discussing these issues will help scientists who may not routinely work with public officials navigate an unfamiliar situation.

An introduction and practical guide to use of the Soil-Vegetation Inventory Method (SVIM) data

Released August 09, 2018 10:21 EST

2018, Rangeland Ecology and Management

Brittany S. Barker, David S. Pilliod, Justin Welty, Robert S. Arkle, Michael G. "Sherm" Karl, Gordon R. Toevs

Long-term vegetation dynamics across public rangelands in the western United States are not well understood because of the lack of large-scale, readily available historic datasets. The Bureau of Land Management’s Soil-Vegetation Inventory Method (SVIM) program was implemented between 1977 and 1983 across 14 western states, but the data have not been easily accessible. We introduce the SVIM vegetation cover dataset in a georeferenced, digital format; summarize how the data were collected; and discuss potential limitations and biases. We demonstrate how SVIM data can be compared with contemporary monitoring datasets to quantify changes in vegetation associated with wildfire and the abundance of exotic invasive species. Specifically, we compare SVIM vegetation cover data with cover data collected by BLM’s Assessment, Inventory, and Monitoring (AIM) program (2011–2016) in a focal area in the northern Great Basin. We address issues associated with analyzing and interpreting data from these distinct programs, including differences in survey methodsand potential biases introduced by spatial and temporal variation in sampling. We compared SVIM and AIM survey methods at 44 plots and found that percent cover estimates had high correspondence for all measured functional groups. Comparisons between historic SVIM data and recent AIM data documented significant declines in the occupancy and cover of native shrubs and native perennial forbs, and a significant increase in exotic annual forbs. Wildfire was a driver of change for some functional groups, with greater change occurring in AIM plots that burned between the two time periods compared with those that did not. Our results are consistent with previous studies showing that many native shrub-dominated plant communities in the Great Basin have been replaced by exotic annuals. Our study demonstrates that SVIM data will be an important resource for researchers interested in quantifying vegetation change through time across public rangelands in the western United States.

Evaluation of the effects of changes in the timing of water-level drawdowns on the export of phosphorus from Little St. Germain Lake, Wisconsin

Released August 09, 2018 08:45 EST

2018, Scientific Investigations Report 2018-5078

Eric D. Dantoin, Dale M. Robertson

Little St. Germain Lake is a 978-acre, multibasin lake in Vilas County, Wisconsin. In the interest of improving its water quality, the Little St. Germain Lake Protection and Rehabilitation District initiated a cooperative study with the U.S. Geological Survey to describe the current phosphorus input into and export from Little St. Germain Lake and evaluate how water releases at different times of the year could affect the amount of phosphorus being released from the lake, potentially affecting water quality in the lake. Approximately 780 pounds per year of phosphorus are exported out of the lake, which is about 80 percent of that contributed to the lake by Muskellunge Creek. By focusing the release of water to times when phosphorus concentrations near the outlet of the lake are highest, export of phosphorus from the lake could increase by about 60 to 80 pounds annually. This is equivalent to reducing phosphorus contributions from Muskellunge Creek by about 7 to 9 percent. Increasing phosphorus export from the lake should improve the long-term water-quality of the lake, especially in the southern basins of the lake.

Manure and fertilizer inputs to land in the Chesapeake Bay watershed, 1950–2012

Released August 09, 2018 08:45 EST

2018, Scientific Investigations Report 2018-5022

Jennifer L.D. Keisman, Olivia H. Devereux, Andrew E. LaMotte, Andrew J. Sekellick, Joel D. Blomquist

Understanding changing nutrient concentrations in surface waters requires quantitative information on changing nutrient sources in contributing watersheds. For example, the proportion of nutrient inputs reaching streams and rivers is directly affected by when and where those nutrients enter the landscape. The goal of this report is to contribute to the U.S. Geological Survey’s efforts to describe spatial and temporal patterns in nutrient inputs to the landscape in the Chesapeake Bay watershed, thereby informing efforts to understand changes in riverine and estuarine conditions. The magnitude, spatial variability, and changes over time in nutrient inputs from manure and fertilizer were evaluated in the context of changes in land use and agricultural practices from 1950 through 2012 at three spatial scales: the entire Chesapeake Bay watershed, the 53 8-digit hydrologic units (HUC8s) that are contained within the watershed, and a set of 7 regions that were determined by aggregating geographically similar HUC8s. The expected effect of agricultural best management practices (BMPs) on agricultural nutrient inputs from 1985 through 2012 was also investigated. Nitrogen (N) and phosphorus (P) inputs from manure increased gradually over time at the scale of the entire watershed. Fertilizer-N inputs showed steeper increases, with greater inter-annual fluctuations. Fertilizer-P inputs were less variable, increasing moderately from 1950 through the mid-1970s, and declining thereafter. Nutrient inputs and farming practices varied geographically within the watershed, with implications for the potential impact of these inputs on downstream water quality and ecosystem health. Both temporal and spatial patterns in the intensity of agricultural nutrient inputs were consistent with the magnitude and concentration of livestock and poultry populations and the intensity of row crop agriculture. Reported implementation of the animal and land-use change BMPs that were evaluated were expected to have little effect on agricultural N inputs. Animal BMPs were expected to have a more measurable impact on manure-P inputs, particularly in areas with large poultry populations. Understanding these patterns is important for explaining the changes that have been observed in nutrient loads to the rivers and streams of the Chesapeake Bay watershed, and their impacts on the water quality and ecosystem health of Chesapeake Bay itself.

Variations on a method for evaluating decadal-scale changes in the groundwater quality of two GAMA coastal study units 2004–14, California GAMA Priority Basin Project

Released August 08, 2018 13:06 EST

2018, Scientific Investigations Report 2018-5088

Robert Kent

Decadal changes in groundwater quality in two study units on the north-central California coast were evaluated by the Priority Basin Project (PBP) of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. Groundwater samples collected from wells during 2004–05 were compared on a pair-wise basis to samples collected from the same wells during 2014. The data set consisted of paired-samples from 50 public supply wells in 2 GAMA-PBP study units (25 wells each in the North San Francisco Bay and the Monterey Bay and Salinas Valley Basins), with analytical results for 160 water-quality constituents. Statistical analysis was done on grouped results for the 59 constituents that were detected in at least 10 percent of the samples during either sampling period to evaluate decadal-scale change by a step-trend analysis.

The data for both of the sampling periods were processed three different ways, resulting in three variations of the paired results to be submitted for statistical analyses. The first evaluation method variation processed data only to facilitate comparison of data when one or both of the results was a non-detection. The second and third variations applied the additional requirement that differences between initial and decadal-sample results exceed a defined threshold to prevent small differences from supporting the conclusion of a step trend. One method for setting the difference threshold between initial-sampling and resampling results is based on criteria used by the GAMA-PBP to determine whether or not replicate results are acceptable. The other difference-threshold-setting method uses a calculated confidence interval around each result based on demonstrated analytical variability for the constituents during each sampling period. Finally, constituents for which decadal-scale changes were statistically significant were identified using the Wilcoxon-Pratt signed-rank test on each of the three evaluation method variations.

Step trends were identified by at least 1 of the 3 method variations for 33 constituents. After considering other factors, however, such as water-quality context and the results of quality-control samples, it was concluded that decadal changes were meaningful for 14 constituents in at least 1 of the 2 study units. Constituents for which step trends indicated meaningful increases were dissolved oxygen, total nitrogen, nitrate, orthophosphate, calcium, chloride, sulfate, iron, and lithium. Constituents for which step trends indicated meaningful decreases were temperature, arsenic, lead, the isotopic ratio of carbon-13, and tritium.

Geologic framework and hydrogeology of the Rio Rico and Nogales 7.5’ quadrangles, upper Santa Cruz Basin, Arizona, with three-dimensional hydrogeologic model

Released August 08, 2018 12:05 EST

2018, Scientific Investigations Report 2018-5062

William R. Page, Mark W. Bultman, D. Paco VanSistine, Christopher M. Menges, Floyd Gray, Michael P. Pantea

Rapid population growth and declining annual recharge to aquifers in the upper Santa Cruz Basin area of southern Arizona, have increased the demand for additional groundwater resources. This demand is predicted to escalate in the future because of higher temperatures, longer droughts, less aquifer recharge, and decreased river and stream base flow. We conducted geologic studies to help evaluate and better understand groundwater resources in the basin. Results of these studies are presented in this report, which summarizes the basin geologic framework and hydrogeology, and presents a threedimensional (3D) hydrogeologic model for the Rio Rico and Nogales 7.5′ quadrangles. Three major hydrogeologic units are displayed in the 3D model; a lower basement confining unit, consisting of Jurassic, Cretaceous, and Tertiary (Paleocene and Oligocene) rocks; a middle unit composed entirely of the Miocene Nogales Formation; and an upper unit consisting of late Miocene to Holocene surficial deposits. The Nogales Formation and the late Miocene to Holocene sediments are the main aquifers in the upper Santa Cruz Basin. The 3D model integrates the hydrogeologic units and faults to define the geometry, structure, and thickness of the aquifer system that provides water to Nogales and surrounding communities of southernmost Arizona. The report includes an EarthVision 3D Viewer, consisting of software enabling the user to view data interactively in 3D space to help explain the internal complexities of the basin geometry, structure, stratigraphy, and hydrology. The 3D model is a synthesis of geologic data from geologic maps, cross sections, and lithologic descriptions and interpretations; and geophysical data including gravity, magnetic data, and airborne electromagnetic data.

Hydraulic modeling and flood-inundation mapping for the Huron River and Ore Lake Tributary, Livingston County, Michigan

Released August 08, 2018 10:15 EST

2018, Scientific Investigations Report 2018-5048

Julia G. Prokopec

Digital flood-inundation maps for an 8-mile (mi) reach of the Huron River near Hamburg, Michigan (station number 04172000), from downstream of Rickett Road to Strawberry Lake, were created by the U.S. Geological Survey (USGS), in cooperation with Green Oak and Hamburg Townships, Michigan, and the U.S. Army Corps of Engineers. The flood-inundation maps also include a 1.16-mi reach of the Ore Lake Tributary until it joins the Huron River, approximately 2.22 mi downstream of Rickett Road. The flood-inundation maps, which can be accessed through the USGS Flood Inundation Mapping Science website at, depict estimates of the areal extent and depth of flooding corresponding to selected water levels (stages) at the USGS streamgage on the Huron River near Hamburg, Michigan (station number 04172000). Near real-time stages at this streamgage may be obtained on the Internet from the USGS National Water Information System at or the National Weather Service (NWS) Advanced Hydrologic Prediction Service at http:/ The NWS Advanced Hydrologic Prediction Service also provides forecasted flood hydrographs at this website.

Flood profiles were computed for the stream reach by means of a one-dimensional step-backwater model. The hydraulic model was calibrated by using the current stage-discharge relation at the Huron River near Hamburg, Mich., streamgage and was calibrated to water levels determined with stage sensors (pressure transducers) temporarily deployed along the stream reach. The hydraulic model was used to compute a set of water-surface profiles for flood stages ranging from 7.0 to 10.5 feet (ft). This range represents stages just above 6.0 (bankfull) to 2.04 ft above the maximum recorded stage at the USGS streamgage on the Huron River near Hamburg, Mich. (station number 04172000). The computed water-surface profiles were then combined with a Geographic Information System digital elevation model (derived from light detection and ranging [lidar] data having a 0.49-ft vertical accuracy and 3.8-ft horizontal resolution) to delineate the area flooded at each water level.

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

Assessment of water resources in areas that affect the habitat of the endangered Hine’s emerald dragonfly in the Lower Des Plaines River Valley, Illinois

Released August 08, 2018 10:12 EST

2018, Scientific Investigations Report 2018-5074

Robert T. Kay, Amy M. Gahala, Clinton Bailey

Review of previous investigations indicates that potential decreases in groundwater recharge and increased groundwater extraction in the vicinity of the Lower Des Plaines River Valley in Will County, Illinois, may reduce the amount of groundwater flow in the Silurian aquifer in this area. Groundwater discharge from the Silurian aquifer to wetlands in the Lower Des Plaines River Valley plays an important role in sustaining the habitat of the endangered Hine’s emerald dragonfly (Somatochlora hineana). Groundwater modeling performed by previous investigators indicates that increasing the amount of water pumped from the aquifer in support of expanded quarry operations near the Lockport Prairie Nature Preserve has the potential to reduce groundwater discharge to the most productive Hine’s emerald dragonfly habitats in Illinois, potentially degrading the habitat. Model simulations indicate that mitigation procedures designed to artificially enhance groundwater recharge in the vicinity of dragonfly habitats near the Lockport Prairie Nature Preserve are likely to offset the effects of increased pumping. Several areas with smaller, often intermittent populations of Hine’s emerald dragonflies have been identified in other parts of the Lower Des Plaines River Valley and elsewhere in Illinois. Human activities have the potential to produce changes in hydrology and water quality that can threaten all of these habitats.

Effects of local shoreline and subestuary watershed condition on waterbird community integrity: Influences of geospatial scale and season in the Chesapeake Bay

Released August 07, 2018 16:31 EST

2018, Estuaries and Coasts (41) 207-222

Diann J. Prosser, Jessica L. Nagel, Shay Howlin, Paul Marban, Daniel D. Day, R. Michael Erwin

In many coastal regions throughout the world, there is increasing pressure to harden shorelines to protect human infrastructures against sea level rise, storm surge, and erosion. This study examines waterbird community integrity in relation to shoreline hardening and land use characteristics at three geospatial scales: (1) the shoreline scale characterized by seven shoreline types: bulkhead, riprap, developed, natural marsh, Phragmites-dominated marsh, sandy beach, and forest; (2) the local subestuary landscape scale including land up to 500 m inland of the shoreline; and (3) the watershed scale >500 m from the shoreline. From 2010 to 2014, we conducted waterbird surveys along the shoreline and open water within 21 subestuaries throughout the Chesapeake Bay during two seasons to encompass post-breeding shorebirds and colonial waterbirds in late summer and migrating and wintering waterfowl in late fall. We employed an Index of Waterbird Community Integrity (IWCI) derived from mean abundance of individual waterbird species and scores of six key species attributes describing each species’ sensitivity to human disturbance, and then used this index to characterize communities in each subestuary and season. IWCI scores ranged from 14.3 to 19.7. Multivariate regression model selection showed that the local shoreline scale had the strongest influence on IWCI scores. At this scale, percent coverage of bulkhead and Phragmites along shorelines were the strongest predictors of IWCI, both with negative relationships. Recursive partitioning revealed that when subestuary shoreline coverage exceeded thresholds of approximately 5% Phragmites or 8% bulkhead, IWCI scores decreased. Our results indicate that development at the shoreline scale has an important effect on waterbird community integrity, and that shoreline hardening and invasive Phragmites each have a negative effect on waterbirds using subestuarine systems.

A novel technique for isolating DNA from Tempus™ blood RNA tubes after RNA isolation

Released August 07, 2018 16:28 EST

2018, BMC Research Notes (11) 1-5

Jason A. Ferrante, Michelle R. Giles, Emily Benzie, Margaret Hunter


We use Tempus blood RNA tubes (Applied Biosystems) during health assessments of American moose (Alces alces spp.) as a minimally invasive means to obtain RNA. Here we describe a novel protocol to additionally isolate high-quality DNA from the supernatant remaining after the RNA isolation methodology. Metrics used to qualify DNA quality included measuring the concentration, obtaining a DNA integrity number from a genomic DNA ScreenTape assay (Agilent), and running the isolated DNA on an agarose gel.


Of the 23 samples analyzed, the average DNA concentration was 121 ng/µl (range 4–337 ng/µl) and a genomic DNA ScreenTape assay of seven samples indicated high DNA integrity values for 6 of the 7 samples (range 9.1–9.4 out of 10). Of the DNA sent for genotyping by sequencing, all proved to be of sufficient integrity to yield high-quality next-generation sequence results. We recommend this simple procedure to maximize the yield of both RNA and DNA from blood samples.

Using partial aggregation in spatial capture recapture

Released August 07, 2018 16:23 EST

2018, Methods in Ecology and Evolution (9) 1896-1907

Cyril Milleret, Pierre Dupont, Henrik Broseth, Jonas Kindberg, J. Andrew Royle, Richard Bischof

  1. Spatial capture–recapture (SCR) models are commonly used for analysing data collected using noninvasive genetic sampling (NGS). Opportunistic NGS often leads to detections that do not occur at discrete detector locations. Therefore, spatial aggregation of individual detections into fixed detectors (e.g., centre of grid cells) is an option to increase computing speed of SCR analyses. However, it may reduce precision and accuracy of parameter estimations.
  2. Using simulations, we explored the impact that spatial aggregation of detections has on a trade‐off between computing time and parameter precision and bias, under a range of biological conditions. We used three different observation models: the commonly used Poisson and Bernoulli models, as well as a novel way to partially aggregate detections (Partially Aggregated Binary model [PAB]) to reduce the loss of information after aggregating binary detections. The PAB model divides detectors into K subdetectors and models the frequency of subdetectors with more than one detection as a binomial response with a sample size of K. Finally, we demonstrate the consequences of aggregation and the use of the PAB model using NGS data from the monitoring of wolverine (Gulo gulo) in Norway.
  3. Spatial aggregation of detections, while reducing computation time, does indeed incur costs in terms of reduced precision and accuracy, especially for the parameters of the detection function. SCR models estimated abundance with a low bias (<10%) even at high degree of aggregation, but only for the Poisson and PAB models. Overall, the cost of aggregation is mitigated when using the Poisson and PAB models. At the same level of aggregation, the PAB observation model out‐performs the Bernoulli model in terms of accuracy of estimates, while offering the benefits of a binary observation model (less assumptions about the underlying ecological process) over the count‐based model.
  4. We recommend that detector spacing after aggregation does not exceed 1.5 times the scale‐parameter of the detection function in order to limit bias. We recommend the use of the PAB observation model when performing spatial aggregation of binary data as it can mitigate the cost of aggregation, compared to the Bernoulli model.

Real-time decision-making during emergency disease outbreaks

Released August 07, 2018 16:12 EST

2018, PLOS Computational Biology (14) 1-18

William J. M. Probert, Chris P. Jewell, Marleen Werkman, Christopher.J. Fonnesbeck, Yoshitaka Goto, Michael C. Runge, Satoshi Sekiguchi, Katriona Shea, Matt J. Keeling, Matthew J. Ferrari, Michael J. Tildesley

In the event of a new infectious disease outbreak, mathematical and simulation models are commonly used to inform policy by evaluating which control strategies will minimize the impact of the epidemic. In the early stages of such outbreaks, substantial parameter uncertainty may limit the ability of models to provide accurate predictions, and policymakers do not have the luxury of waiting for data to alleviate this state of uncertainty. For policymakers, however, it is the selection of the optimal control intervention in the face of uncertainty, rather than accuracy of model predictions, that is the measure of success that counts. We simulate the process of real-time decision-making by fitting an epidemic model to observed, spatially-explicit, infection data at weekly intervals throughout two historical outbreaks of foot-and-mouth disease, UK in 2001 and Miyazaki, Japan in 2010, and compare forward simulations of the impact of switching to an alternative control intervention at the time point in question. These are compared to policy recommendations generated in hindsight using data from the entire outbreak, thereby comparing the best we could have done at the time with the best we could have done in retrospect.

Our results show that the control policy that would have been chosen using all the data is also identified from an early stage in an outbreak using only the available data, despite high variability in projections of epidemic size. Critically, we find that it is an improved understanding of the locations of infected farms, rather than improved estimates of transmission parameters, that drives improved prediction of the relative performance of control interventions. However, the ability to estimate undetected infectious premises is a function of uncertainty in the transmission parameters. Here, we demonstrate the need for both real-time model fitting and generating projections to evaluate alternative control interventions throughout an outbreak. Our results highlight the use of using models at outbreak onset to inform policy and the importance of state-dependent interventions that adapt in response to additional information throughout an outbreak.

Impacts of coastal land use and shoreline armoring on estuarine ecosystems: An introduction to a special issue

Released August 07, 2018 16:08 EST

2018, Estuaries and Coasts (41) 2-18

Diann J. Prosser, Thomas E. Jordan, Jessica L. Nagel, Rochelle D. Seitz, Donald E. Weller, Dennis F. Whigham

The nearshore land-water interface is an important ecological zone that faces anthropogenic pressure from development in coastal regions throughout the world. Coastal waters and estuaries like Chesapeake Bay receive and process land discharges loaded with anthropogenic nutrients and other pollutants that cause eutrophication, hypoxia, and other damage to shallow-water ecosystems. In addition, shorelines are increasingly armored with bulkhead (seawall), riprap, and other structures to protect human infrastructure against the threats of sea-level rise, storm surge, and erosion. Armoring can further influence estuarine and nearshore marine ecosystem functions by degrading water quality, spreading invasive species, and destroying ecologically valuable habitat. These detrimental effects on ecosystem function have ramifications for ecologically and economically important flora and fauna. This special issue of Estuaries and Coasts explores the interacting effects of coastal land use and shoreline armoring on estuarine and coastal marine ecosystems. The majority of papers focus on the Chesapeake Bay region, USA, where 50 major tributaries and an extensive watershed (~ 167,000 km2), provide an ideal model to examine the impacts of human activities at scales ranging from the local shoreline to the entire watershed. The papers consider the influence of watershed land use and natural versus armored shorelines on ecosystem properties and processes as well as on key natural resources.

The case for mean rupture distance in ground‐motion estimation

Released August 07, 2018 16:05 EST

2018, Bulletin of the Seismological Society of America

Eric M. Thompson, Annemarie S. Baltay

This article advocates for the use of mean rupture distances that we contend are more physically representative of the distance to an earthquake and are simpler than minimum distances. Many current ground‐motion models (GMMs) rely on numerous modifications of minimum rupture distances to accurately model near‐source ground motions. These modifications, that include additional distance definitions and saturation terms, result in complicated functional forms and are often not easily understood on a seismological basis, such as the magnitude‐dependent near‐fault saturation term. The use of mean distance represents the location of a station in relation to the entire rupture plane and results in a simpler, more physically meaningful GMM that models near‐source ground motion as accurately as other GMMs that have more inputs and more complex functional forms. We demonstrate the use of mean distance by developing a GMM for shallow‐crustal earthquakes with the Next Generation Attenuation‐West2 (NGA‐West2) project database. Specifically, we use the generalized mean distance, also known as the power mean, in which the power varies with frequency. We show that this new GMM fits the NGA‐West2 database as well as the NGA‐West2 GMMs and exhibits similar near‐source amplitude scaling. An additional benefit of mean distance is that it can provide a mechanism to account for spatially variable slip. We prospectively validate this GMM against the 2016 M 7.8 Kaikōura, New Zealand, earthquake, which was not used in model development. To better understand the magnitude dependence of geometrical spreading, we employ a simple conceptual model based on fundamental principles to show that the GMM is consistent with common seismological understanding.

Examination of contaminant exposure and reproduction of ospreys (Pandion haliaetus) nesting in Delaware Bay and River in 2015

Released August 07, 2018 12:26 EST

2018, Science of the Total Environment (639) 596-607

Barnett A. Rattner, Rebecca S. Lazarus, Thomas G. Bean, Peter C. McGowan, Carl R. Callahan, Richard A. Erickson, Robert Hale

A study of ospreys (Pandion haliaetus) nesting in the coastal Inland Bays of Delaware, and the Delaware Bay and Delaware River in 2015 examined spatial and temporal trends in contaminant exposure, food web transfer and reproduction. Concentrations of organochlorine pesticides and metabolites, polychlorinated biphenyls (PCBs), coplanar PCB toxic equivalents, polybrominated diphenyl ethers (PBDEs) and other flame retardants in sample eggs were generally greatest in the Delaware River. Concentrations of legacy contaminants in 2015 Delaware Bay eggs were lower than values observed in the 1970s through early 2000s. Several alternative brominated flame retardants were rarely detected, with only TBPH [bis(2-ethylhexyl)-tetrabromophthalate)] present in 5 of 27 samples at <5 ng/g wet weight. No relation was found between p,p′-DDE, total PCBs or total PBDEs in eggs with egg hatching, eggs lost from nests, nestling loss, fledging and nest success. Osprey eggshell thickness recovered to pre-DDT era values, and productivity was adequate to sustain a stable population. Prey fish contaminant concentrations were generally less than those in osprey eggs, with detection frequencies and concentrations greatest in white perch (Morone americana) from Delaware River compared to the Bay. Biomagnification factors from fish to eggs for p,p′-DDE and total PCBs were generally similar to findings from several Chesapeake Bay tributaries. Overall, findings suggest that there have been improvements in Delaware Estuary waterbird habitat compared to the second half of the 20th century. This trend is in part associated with mitigation of some anthropogenic contaminant threats.

Mechanisms of earthquake‐induced chemical and fluid transport to carbonate groundwater springs after earthquakes

Released August 06, 2018 16:56 EST

2018, Water Resources Research

Michael R. Rosen, Gilberto Binda, Claire Archer, Andrea Pozzi, Alessandro Michetti, Paula Noble

Mechanisms by which hydrochemical changes occur after earthquakes are not well documented. We use the 2016–2017 central Italy seismic sequence, which caused notable hydrochemical transient variations in groundwater springs to address this topic, with special reference to effects on fractured carbonate aquifers. Hydrochemistry measured before and after the earthquakes at four springs at varying distances from the epicenters all showed immediate postmainshock peaks in trace element concentrations but little change in major elements. Most parameters returned to preearthquake values before the last events of the seismic sequence. The source of solutes, particularly trace elements, is longer residence time pore water stored in slow‐moving fractures or abandoned karstic flow paths. These fluids were expelled into the main flow paths after an increase in pore pressure, hydraulic conductivity, and shaking from coseismic aquifer stress. The weak response to the later earthquakes is explained by progressive depletion of high solute fluids as earlier shocks flushed out the stored fluids in the fractures. Spring δ13CDIC values closest to a deep magma source to the west became enriched relative to preearthquake values following the 24 August event. This enrichment indicates input from deeply sourced dissolved CO2 gas after dilation of specific fault conduits. Differences in carbon isotopic responses between springs are attributed to proximity to the deep gaseous CO2 source. Most of the transient chemical changes seen in the three fractured carbonate aquifers are attributed to local shaking and emptying of isolated pores and fractures and are not from rapid upward movement of deep fluids.

Tracing the cycling and fate of the munition, Hexahydro-1,3,5-trinitro-1,3,5-triazine in a simulated sandy coastal marine habitat with a stable isotopic tracer, 15N-[RDX]

Released August 06, 2018 16:02 EST

2019, Science of the Total Environment (647) 369-378

Thivanka Ariyarathna, Mark Ballentine, Penny Vlahos, Richard W. Smith, Christopher Cooper, John Karl Böhlke, Stephen Fallis, Thomas J. Groshens, Craig R. Tobias

Coastal marine habitats become contaminated with the munitions constituent, Hexahydro-1,3,5-trinitro-1,3,5-trazine (RDX), via military training, weapon testing and leakage of unexploded ordnance. This study used 15N labeled RDX in simulated aquarium-scale coastal marine habitat containing seawater, sediment, and biota to track removal pathways from surface water including sorption onto particulates, degradation to nitroso-triazines and mineralization to dissolved inorganic nitrogen (DIN). The two aquaria received continuous RDX inputs to maintain a steady state concentration (0.4 mg L−1) over 21 days. Time series RDX and nitroso-triazine concentrations in dissolved (surface and porewater) and sorbed phases (sediment and suspended particulates) were analyzed. Distributions of DIN species (ammonium, nitrate + nitrite and dissolved N2) in sediments and overlying water were also measured along with geochemical variables in the aquaria. Partitioning of RDX and RDX-derived breakdown products onto surface sediment represented 13% of the total added 15N as RDX (15N-[RDX]) equivalents after 21 days. Measured nitroso-triazines in the aquaria accounted for 6–13% of total added 15N-[RDX]. 15N-labeled DIN was found both in the oxic surface water and hypoxic porewaters, showing that RDX mineralization accounted for 34% of the 15N-[RDX] added to the aquaria over 21 days. Labeled ammonium (15NH4+, found in sediment and overlying water) and nitrate + nitrite (15NOX, found in overlying water only) together represented 10% of the total added 15N-[RDX]. The production of 15N labeled N2(15N2), accounted for the largest individual sink during the transformation of the total added 15N-[RDX] (25%). Hypoxic sediment was the most favorable zone for production of N2, most of which diffused through porous sediments into the water column and escaped to the atmosphere.

The confluences of ideas leading to, and the flow of ideas emerging from, individual-based modeling of riverine fishes

Released August 06, 2018 14:53 EST

2018, Ecological Modelling (384) 341-352

Henriette I. Jager, Donald L. DeAngelis

In this review article, we trace the history of events leading to the development of individual-based models (IBMs) to represent aquatic organisms in rivers and streams. As a metaphor, we present this history as a series of confluences between individual scientists (tributaries) sharing ideas. We describe contributions of these models to science and management. One iconic feature of river IBMs is the linkage between flow and the physical habitat experienced by individual animals, and the first model that focused on this linkage is briefly described. We continue by reviewing the contributions of riverine IBMs to eight broad areas of scientific inquiry. The first four areas include research to understand 1) the effects of flow regimes on fish populations, 2) species interactions (e.g., size-mediated competition and predation), 3) fish movement and habitat selection, and 4) contaminant and water quality impacts on populations. Next, we review research using IBMs 5) to guide conservation biology of imperiled taxa through population viability analysis, including research 6) to understand river fragmentation by dams and reconnection, 7) to understand genetic outcomes for riverine metapopulations, and 8) to anticipate the future effects of temperature and climate change. This rich body of literature has contributed to both theoretical insights (e.g., about animal behavior and life history) and applied insights (e.g., population-level effects of flow regimes, temperature, and the effects of hydropower and other industries that share rivers with aquatic biota). We finish by exploring promising branches that lie ahead in the braided, downstream channel that represents future river modeling research.

Exploring the pathology of an epidermal disease affecting a circum-Antarctic sea star

Released August 06, 2018 12:57 EST

2018, Scientific Reports (8) 1-12

Laura Nunez-Pons, Thierry M. Work, Carlos Angulo-Preckler, Juan Moles, Conxita Avila

Over the past decade, unusual mortality outbreaks have decimated echinoderm populations over broad geographic regions, raising awareness globally of the importance of investigating such events. Echinoderms are key components of marine benthos for top-down and bottom-up regulations of plants and animals; population declines of these individuals can have significant ecosystem-wide effects. Here we describe the first case study of an outbreak affecting Antarctic echinoderms and consisting of an ulcerative epidermal disease affecting ~10% of the population of the keystone asteroid predator Odontaster validus at Deception Island, Antarctica. This event was first detected in the Austral summer 2012–2013, coinciding with unprecedented high seawater temperatures and increased seismicity. Histological analyses revealed epidermal ulceration, inflammation, and necrosis in diseased animals. Bacterial and fungal alpha diversity was consistently lower and of different composition in lesioned versus unaffected tissues (32.87% and 16.94% shared bacterial and fungal operational taxonomic units OTUs respectively). The microbiome of healthy stars was more consistent across individuals than in diseased specimens suggesting microbial dysbiosis, especially in the lesion fronts. Because these microbes were not associated with tissue damage at the microscopic level, their contribution to the development of epidermal lesions remains unclear. Our study reveals that disease events are reaching echinoderms as far as the polar regions thereby highlighting the need to develop a greater understanding of the microbiology and physiology of marine diseases and ecosystems health, especially in the era of global warming.

Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest

Released August 06, 2018 12:55 EST

2018, Molecular Ecology

Jeanne M. Robertson, Melanie A. Murphy, Christopher Pearl, Michael J. Adams, Monica I. Paez-Vacas, Susan M. Haig, David S. Pilliod, Andrew Storfer, W. Chris Funk

Comparative landscape genetics has uncovered high levels of variability in which landscape factors affect connectivity among species and regions. However, the relative importance of species traits versus environmental variation for predicting landscape patterns of connectivity is unresolved. We provide evidence from a landscape genetics study of two sister taxa of frogs, the Oregon spotted frog (Rana pretiosa) and the Columbia spotted frog (Rana luteiventris) in Oregon and Idaho, USA. Rana pretiosa is relatively more dependent on moisture for dispersal than R. luteiventris, so if species traits influence connectivity, we predicted that connectivity among R. pretiosa populations would be more positively associated with moisture than R. luteiventris. However, if environmental differences are important drivers of gene flow, we predicted that connectivity would be more positively related to moisture in arid regions. We tested these predictions using eight microsatellite loci and gravity models in two R. pretiosaregions and four R. luteiventris regions (= 1,168 frogs). In R. pretiosa, but not R. luteiventris, connectivity was positively related to mean annual precipitation, supporting our first prediction. In contrast, connectivity was not more positively related to moisture in more arid regions. Various temperature metrics were important predictors for both species and in all regions, but the directionality of their effects varied. Therefore, the pattern of variation in drivers of connectivity was consistent with predictions based on species traits rather than on environmental variation.

Mapping and measuring aeolian sand dunes with photogrammetry and LiDAR from unmanned aerial vehicles (UAV) and multispectral satellite imagery on the Paria Plateau, AZ, USA

Released August 06, 2018 12:50 EST

2018, Geomorphology (319) 174-185

Daniel Solazzo, Joel B. Sankey, Temuulen T. Sankey, Seth M. Munson

The Paria Plateau is a potentially important but relatively unstudied aeolian sand source area in the Grand Canyon region of Arizona, USA. This study used unmanned aerial vehicle(UAV) - based LiDAR and structure-from-motion (SfM) photogrammetry to produce high-resolution topographic models of aeolian dunes on the plateau. We combined the dune topography data with a high-resolution satellite image maximum likelihood classification (producer's accuracy = 87.2%) to quantify potential aeolian sand source areas across the 958 km2 plateau. We mapped all the unvegetated active aeolian dunes on the plateau and estimate they contain 24 Tg of sand, and could, therefore, be a proportionately important regional sand source considering the annual sand loads of the downwind Paria River at its confluence with the Colorado River are generally <1 Tg. The results and data from this study could be useful for future investigations that wish to explicitly link aeolian sand on the Paria Plateau to downwind sediment dynamics in the region. The methodology for UAV and satellite remote sensing that we demonstrate could be applied to quantify sand at large geographic extents in other aeolian environments around the world.

Phenology of hatching, emergence, and end-of-season body size in young-of-year Coho Salmon in thermally contrasting streams draining the Copper River Delta, Alaska

Released August 06, 2018 12:33 EST

2018, Canadian Journal of Fisheries and Aquatic Sciences

Emily Y. Campbell, Jason B. Dunham, Gordon H. Reeves, Steve M. Wondzell

Phenology can be linked to individual fitness, particularly in strongly seasonal environments where the timing of events have important consequences for growth, condition, and survival. We studied the phenology of Coho Salmon hatching and emergence in streams with contrasting thermal variability, but in close geographic proximity. Following emergence, we tracked body sizes of cohorts of young-of-year fish until the end of the growing season. Hatch and emergence timing occurred at the same time among streams with marked variability in thermal regimes. We demonstrate that this can be explained in part by the thermal units accumulated during embryo development. At the end of the first growing season there were some differences in body size, however overall fish size among streams were similar despite strong differences in thermal regimes. Collectively these results provide novel insights into the interactions between environmental variability and the early life-history stages of Coho Salmon furthering our understanding of the consequences of phenology on growth and survival for individuals within the critical first summer of life.

An exploratory Bayesian network for estimating the magnitudes and uncertainties of selected water-quality parameters at streamgage 03374100 White River at Hazleton, Indiana, from partially observed data

Released August 06, 2018 12:30 EST

2018, Scientific Investigations Report 2018-5053

David J. Holtschlag

An exploratory discrete Bayesian network (BN) was developed to assess the potential of this type of model for estimating the magnitudes and uncertainties of an arbitrary subset of unmeasured water-quality parameters given the measured complement of parameters historically measured at a U.S. Geological Survey streamgage. Water-quality data for 27 water-quality parameters from 596 discrete measurements at U.S. Geological Survey streamgage 03374100 White River at Hazleton, Indiana, were used to develop this BN. Data for each of the water-quality parameters were discretized into five intervals based on the quintiles of the measured values. The 596 discrete measurements were randomly partitioned into a training set with 80 percent of the data and a testing set with 20 percent of the data to identify, estimate, and assess the training and testing accuracy of the Bayesian network.

A BN with 28 nodes was formed from the 27 water-quality parameters and the month of sample collection. Based on data in the training set, a network with 53 directed edges and month as the target node was identified by minimizing the negative log-likelihood function for all nodes treated, in turn, as the target variable. The edge structure determines the number and magnitude of elements in conditional probability tables associated with all nodes.

The effectiveness of the BN was assessed on the basis of correct classification rates to one of the five discrete intervals, which were computed separately for the training and testing datasets and for two conditioning variable sets. The selected sets of conditioning variables represent two of many possible sets of measured parameters on which to base estimates of unmeasured parameters. The first set includes only the month of sample collection (month), and an expanded set includes month and six other continuously measurable parameters, referred to as the ContMeasSet, all of which were obtained from the discrete data.

Results indicated that the training dataset had average correct classification rates of 41.7- and 61.2-percent rates conditioned on the month and ContMeasSet sets, respectively. The testing dataset had somewhat lower average correct classification rates of 40.8 and 56.5 percent for the two conditioning variable sets. When conditioned on month only, the average correct classification rate for the testing dataset was only slightly lower than the average correct classification rate in the training dataset, indicating little model overfitting. When using the ContMeasSet, however, the average decrease in accuracy between training and testing sets was 4.9 percent. The training and testing datasets and both sets of conditioning variables, however, indicate that the BN would substantially outperform a random assignment model, which would be expected to have a 20-percent correct classification rate. In addition, the edge structure of the BN depicts how information can flow through the network, which may help prioritize parameters for measurement to facilitate estimation of unmeasured parameters. Finally, extension of a static BN, like the one developed in this report, to a dynamic BN may provide a basis for using high-frequency or continuous water-quality data to extend information in time between discrete water-quality samples, and this integration could mitigate some of the limitations of high-frequency and discrete water-quality sampling methods.

Effectiveness of environmental flows for riparian restoration in arid regions: A tale of four rivers

Released August 06, 2018 12:17 EST

2017, Ecological Engineering (106) 695-703

Edward P. Glenn, Pamela L. Nagler, Patrick B. Shafroth, Christopher Jarchow

Environmental flows have become important restoration tools on regulated rivers. However, environmental flows are often constrained by other demands within the river system and thus typically are comprised of smaller water volumes than the natural flows they are meant to replace, which can limit their functional efficacy. We review environmental flow programs aimed at restoring riparian vegetation on four arid zone rivers: the Tarim River in China; the Bill Williams River in Arizona, U.S.; the delta of the Colorado River in Mexico; and the Murrumbidgee River in southern Australia. Our goal is to determine what worked and what did not work to accomplish restoration goals. The lower Tarim River in China formerly formed a “green corridor” across the Taklamakan Desert. The riparian zone deteriorated due to diversion of surface and groundwater for irrigated agriculture. A massive restoration program began in 2000 with release of 1038 million cubic meters of water over the first three years. Groundwater levels rose but the ecological response was less than expected politically, socially and within the scientific community. However, releases continued and by 2015 portions of the original iconic Populus euphratica (Euphrates poplar) forest were reestablished. The natural flow regime of the Bill Williams River was disrupted by construction of a dam in 1968, dramatically reducing peak flows along with associated fluvial processes. As a result, the channel narrowed and riparian vegetation expanded and was comprised largely of an introduced shrub species (Tamarix spp.). Environmental flow releases including small, managed floods and sustained base flows have been implemented since the mid 1990’s to promote establishment and maintenance of native riparian trees (cottonwoods and willows) and have been successful, although in a “downsized” portion of the valley bottom. Experience from the Bill Williams was used to help design the Minute 319 environmental flow in the delta of the Colorado River in 2014. Water was released as a short, one-time pulse during spring with the intent of starting new cohorts of cottonwood and willow. However, fluvial disturbance was limited by the relatively small magnitude pulse, low flows did not continue throughout the growing season in some reaches, native tree recruitment was low, and most of the new plants recruited were Tamarix. The inundated portion of the floodplain did respond with a temporary increase in greenness as measured by satellite vegetation indices, however. The Murrumbidgee River in Australia is a tributary in the Murray-Darling River Basin, which supports iconic red gum (Eucalyptus camaldulensis) forests that depend on near-yearly floods for maintenance. During the recent Millennial Drought (2000–2010) environmental flows were provided on an experimental basis to small portions of the Yanga National Forest to see how much water was needed. As with the Colorado River delta, gains in vegetation vigor as measured by satellite vegetation indices following the flows were temporary. Environmental flows in the Bill Williams were able to restore enough overbank flooding and fluvial disturbance to promote some establishment of new cohorts of trees, but on the Colorado and Murrumbidgee Rivers larger volumes of total flows released over longer periods and targeted restoration will be needed to restore the ecosystems. A measure of success in restoring the Euphrates poplar forest on the Tarim and germinating new chorts of willows on the Bill Williams has been achieved after 15–20 years of environmental flows, but the Colorado River delta and Murrumbidgee Rivers have only received one or two flows. Success in enhancing native trees in the Colorado delta has been achieved in restoration plots, but the Murrumbidgee will require large overbank flows on a continuing schedule to rejuvenate the red gum forest.

Seismic evidence for significant melt beneath the Long Valley Caldera, California, USA

Released August 06, 2018 12:14 EST

2018, Geology

Ashton Flinders, David R. Shelly, Phillip B. Dawson, David P. Hill, Barbara Tripoli, Yang Shen

A little more than 760 ka ago, a supervolcano on the eastern edge of California (United States) underwent one of North America's largest Quaternary explosive eruptions. Over this ~6-day-long eruption, pyroclastic flows blanketed the surrounding ~50 km with more than 1400 km3 of the now-iconic Bishop Tuff, with ashfall reaching as far east as Nebraska. Collapse of the volcano's magma reservoir created the restless Long Valley Caldera. Although no rhyolitic eruptions have occurred in 100 k.y., beginning in 1978, ongoing uplift suggests new magma may have intruded into the reservoir. Alternatively, the reservoir could be approaching final crystallization, with present-day uplift related to the expulsion of fluid from the last vestiges of melt. Despite 40 years of diverse investigations, the presence of large volumes of melt in Long Valley's magma reservoir remain unresolved. Here we show, through full waveform seismic tomography, a mid-crustal zone of low shear-wave velocity. We estimate the reservoir contains considerable quantities of melt, >1000 km3, at melt fractions as high as ~27%. While supervolcanoes like Long Valley are rare, understanding the volume and concentration of melt in their magma reservoirs is critical for determining their potential hazard.

International meeting on sarcoptic mange in wildlife, June 2018, Blacksburg, Virginia, USA

Released August 06, 2018 12:07 EST

2018, Parasites & Vectors (11) 1-10

Francisca Astorga, Scott Carver, Emily S. Almberg, Giovane R. Sousa, Kimberly Wingfield, Kevin D. Niedringhaus, Peach Van Wick, Luca Rossi, Yue Xie, Paul C. Cross, Samer Angelone, Christian Gortázar, Luis E. Escobar

Sarcoptic mange is a globally distributed disease caused by the burrowing mite Sarcoptes scabiei, which also causes scabies in humans. A wide and increasing number of wild mammal species are reported to be susceptible to mange; however, the impacts of the disease in wildlife populations, mechanisms involved in its eco-epidemiological dynamics, and risks to public and ecosystem health are still unclear. Major gaps exist concerning S. scabiei host specificity and the mechanisms involved in the different presentations of the disease, which change between individuals and species. Immunological responses to the mite may have a relevant role explaining these different susceptibilities, as these affect the clinical signs, and consequently, the severity of the disease. Recently, some studies have suggested sarcoptic mange as an emerging threat for wildlife, based on several outbreaks with increased severity, geographical expansions, and novel wild hosts affected. Disease ecology experts convened for the “International Meeting on Sarcoptic Mange in Wildlife” on 4–5 June 2018, hosted by the Department of Fish and Wildlife Conservation at Virginia Tech in Blacksburg, Virginia, USA. The meeting had a structure of (i) pre-workshop review; (ii) presentation and discussions; and (iii) identification of priority research questions to understand sarcoptic mange in wildlife. The workgroup concluded that research priorities should be on determining the variation in modes of transmission for S. scabiei in wildlife, factors associated with the variation of disease severity among species, and long-terms effects of the mange in wildlife populations. In this note we summarize the main discussions and research gaps identified by the experts.

Pliocene erosional pulse and glacier-landscape feedbacks in the western Alaska Range

Released August 06, 2018 12:04 EST

2018, Earth and Planetary Science Letters (497) 62-68

Richard O. Lease

Pliocene–Pleistocene glaciation modified the topography and erosion of most middle- and high-latitude mountain belts, because the evolution of catchment topography controls long-term glacier mass balance and erosion. Hence, characterizing how erosion rates change during repeated glaciations can help test hypothesized glacier erosion-landscape feedbacks across a range of settings. To better understand how glaciations and landscapes coevolve on geologic timescales, I quantify erosion rates in the glaciated western Alaska Range with low-temperature thermochronometric data and modeling. Zircon (U–Th)/He and apatite fission track data suggest mountain-building was underway by the early Miocene. In contrast, lower-temperature apatite (U–Th)/He age-elevation and grain age-kinetic data indicate that erosion accelerated coincident with regional Pliocene glaciation ca. 4 Ma. Furthermore, erosion rates calculated within an eroding half-space indicate slow erosion at a rate ≤0.3 km/m.y. before 4.2 Ma, an initial pulse of rapid erosion at a rate of 1.0–1.6 km/m.y. during 4.2–2.9 Ma, and more moderate erosion at a rate of 0.4–0.7 km/m.y. since 2.9 Ma. The initial erosion pulse suggests a significant transient landscape adjustment to the introduction of efficient glacial erosion. The subsequent decrease in Pleistocene erosion rates is consistent with a negative feedback between continuing glaciation and glacier size/erosivity: If glacial erosion outpaces rock uplift, glacier erosion decreases over time as topography, mass balance, valley gradients, and ice flux are reduced. These findings imply that in areas of moderate rock uplift rates, the onset of local Plio–Pleistocene glaciation may have been punctuated by an initial pulse of rapid landscape change, after which change became more gradual.

Growth stress response to sea level rise in species with contrasting functional traits: A case study in tidal freshwater forested wetlands

Released August 06, 2018 12:01 EST

2018, Environmental and Experimental Botany (155) 378-386

Lu Zhai, Ken W. Krauss, Xin Liu, Jamie A. Duberstein, William H. Conner, Donald L. DeAngelis, Leonel d.S.L Sternberg

With rising sea levels, mortality of glycophytes can be caused by water and nutrient stress under increasing salinity. However, the relative effects of these two stressors may vary by species-specific functional traits. For example, deciduous species, with leaves typically emerging during low salinity periods of the year, may suffer less from water stress than evergreen species. We sampled two woody species with contrasting functional traits: the evergreen and N2-fixing waxmyrtle (Morella cerifera), and the deciduous and non-N2 fixing baldcypress (Taxodium distichum) along a coastal river (South Carolina, USA) showing an increasing pattern of plant mortality along a salinity gradient. We first analyzed oxygen and hydrogen isotope ratios of plant stem water and river water to determine changes in plant source water at different sites. Then we analyzed foliar carbon and nitrogen isotope ratios (δ13C and δ15N) along with nitrogen and phosphorous content (%N and %P) as proxies for the water and nutrient stress. Results showed that: (1) the two species had different water sources at the higher salinity sites; (2) foliar δ15N values of baldcypress decreased with higher salinity while retaining a constant δ13C value, and both of these isotope values were positively related with foliar %P, suggesting greater nutrient stress but minor water stress under high salinity; and (3) foliar δ13C values of waxmyrtle increased with higher salinity while retaining a constant foliar δ15N value, and neither of the values was significantly related to foliar nutrients, suggesting greater water stress but minor nutrient stress under high salinity. The different responses of the two species to high salinity may be related to their differences in leaf phenology and N2-fixation. Our results suggest that nutrient stress, particularly of P, can contribute to stress and eventual high mortality of baldcypress exposed to salt water intrusion.

Piscivore diet shifts and trophic level change after Alewife establishment in Lake Champlain

Released August 03, 2018 15:23 EST

2018, Transactions of the American Fisheries Society

Paul W. Simonin, Lars G. Rudstam, Donna Parrish, Bernard Pientka, Patrick J. Sullivan

Invasions and deliberate introductions of new prey species are likely to affect prey choice and trophic level of resident predators. Rainbow Smelt (Osmerus mordax) and Alewife (Alosa pseudoharengus) are common prey fish species in lakes throughout North America either as native or non‐native species. The establishment of Alewife in the 2000s in a lake with a native Rainbow Smelt population (Lake Champlain) presented an opportunity to study changes in the diet and trophic level of fish already established in the system. Using stable isotope analysis, we found that Alewife became a major component of predator diets, in particular of the diets of Atlantic Salmon (Salmo salar) and Walleye (Sander vitreus). Lake Trout (Salvelinus namaycush) consumed relatively few Alewives. For Walleye (the predator with both pre‐ and post‐Alewife isotope ratios available), the δ15N values decreased significantly from the pre‐Alewife period of the late 1990s, indicating that Walleye feed at lower trophic levels when Alewife are present. Predation on Alewife was correlated with the amount of spatial overlap of predators and prey. Our results show that the introduction of Alewife has altered the predator‐prey linkages in Lake Champlain; alterations that can have major effects on food web structure and trophic cascades.

Granite IP network default route disappearance—Diagnosis and solution

Released August 03, 2018 15:07 EST

2018, Open-File Report 2018-1117

Lawrence M. Baker

The U.S. Geological Survey (USGS) National Strong Motion Project (NSMP) operates numerous strong-motion seismographs to monitor ground shaking and structural response caused by large, nearby earthquakes. This report describes a problem NSMP scientists encountered communicating over the Internet with several Kinemetrics, Inc., Granite strong-motion recorders.

The Granite strong-motion recorders (“Granites”) get into a state where they cannot be reached from the Internet and they cannot reach the Internet, yet they can reach and be reached from the local Ethernet subnet. The reason is that the Internet Protocol (IP) network default route has disappeared; only the local route is available. Diagnosis is complicated by the unpredictability of the circumstances leading to the failure. The failures have happened at several field sites but cannot be reproduced in the lab.

This report describes the IP networking behavior of a Granite system and provides modifications to the Granite Ethernet device drivers to send Ethernet link (carrier) state-change event notifications to the Linux kernel. With these modifications, the Linux netplugd daemon can be configured to properly reconfigure Granite IP networking when the Ethernet interface link state changes.

The influence of angler values, involvement, catch orientation, satisfaction, agency trust, and demographics on support for habitat protection and restoration versus stocking in publicly managed waters

Released August 03, 2018 14:07 EST

2018, Environmental Management

Susan A. Schroeder, David C. Fulton, Eric Altena, Heather Baird, Douglas J. Dieterman, Martin Jennings

Resource managers benefit from knowledge of angler support for fisheries management strategies. Factors including angler values (protection, utilitarian, and dominance), involvement (attraction, centrality, social, identity affirmation, and expression), catch-related motivations (catching some, many, and big fish, and keeping fish), satisfaction, agency trust, and demographics may relate to fisheries management preferences. Using results from a mail survey of Minnesota resident anglers, we explored how these factors were related to budget support for fish stocking relative to habitat protection/restoration. Results suggest that values, angler involvement, catch orientation, satisfaction, total and recent years fishing, age, and education influence relative support for stocking versus habitat protection/restoration. Utilitarian values, angling centrality, an orientation to catch many fish, satisfaction with the number of fish caught, number of recent years fishing, and age positively related to support for stocking over habitat management, while protection values, attraction to angling, total years fishing, and education level were negatively related to relative support for stocking.

Effects of temperature and precipitation on grassland bird nesting success as mediated by patch size

Released August 03, 2018 13:44 EST

2018, Conservation Biology (32) 872-882

Benjamin Zuckerberg, Christine Ribic, Lisa A. McCauley

Grassland birds are declining faster than any other bird guild across North America. Shrinking ranges and population declines are attributed to widespread habitat loss and increasingly fragmented landscapes of agriculture and other land uses that are misaligned with grassland bird conservation. Concurrent with habitat loss and degradation, temperate grasslands have been disproportionally affected by climate change relative to most other terrestrial biomes. Distributions of grassland birds often correlate with gradients in climate, but few researchers have explored the consequences of weather on the demography of grassland birds inhabiting a range of grassland fragments. To do so, we modeled the effects of temperature and precipitation on nesting success rates of 12 grassland bird species inhabiting a range of grassland patches across North America (21,000 nests from 81 individual studies). Higher amounts of precipitation in the preceding year were associated with higher nesting success, but wetter conditions during the active breeding season reduced nesting success. Extremely cold or hot conditions during the early breeding season were associated with lower rates of nesting success. The direct and indirect influence of temperature and precipitation on nesting success was moderated by grassland patch size. The positive effects of precipitation in the preceding year on nesting success were strongest in relatively small grassland patches and had little effect in large patches. Conversely, warm temperatures reduced nesting success in small grassland patches but increased nesting success in large patches. Mechanisms underlying these differences may be patch‐size‐induced variation in microclimates and predator activity. Although the exact cause is unclear, large grassland patches, the most common metric of grassland conservation, appears to moderate the effects of weather on grassland‐bird demography and could be an effective component of climate‐change adaptation.

Land treatment planning tool

Released August 03, 2018 13:12 EST

2018, Fact Sheet 2018-3042

David S. Pilliod, Justing L. Welty, Michelle I. Jeffries, Linda S. Schueck, Thomas J. Zarriello

Land managers make decisions regarding restoration and rehabilitation actions that influence landscapes and ecosystems. Many of these decisions involve soil and vegetation manipulations, often known as land treatments. Historically, treatments were planned on a case by case basis with decisions derived from personal experience of past successes or failures. Current adaptive management strategies require a more structured and robust approach to the planning and implementation of land treatments.

The U.S. Geological Survey partnered with the Bureau of Land Management to create the Land Treatment Planning Tool to facilitate adaptive management of land treatments. The Planning Tool taps into a wealth of information about past treatments in the Land Treatment Digital Library (LTDL,

The Planning Tool is designed for use by resource managers during the land treatment planning stage. This tool summarizes environmental characteristics of planned treatment areas and facilitates adaptive management practices by comparing those characteristics to similar legacy treatments.

Brackish groundwater and its potential as a resource in the southwestern United States

Released August 03, 2018 10:55 EST

2018, Fact Sheet 2018-3010

David W. Anning, Kimberly R. Beisner, Angela P. Paul, Jennifer S. Stanton, Susan A. Thiros

Secure, reliable, and sustainable water resources are fundamental to food production, energy independence, and the health of humans and ecosystems. But the large-scale development of fresh groundwater resources has stressed aquifers in some areas, causing declines in the amount of groundwater in storage and decreases in discharge to surface-water bodies like rivers and springs (Reilly and others, 2008). In some parts of the southwestern United States, the water supply is not adequate to meet demand without substantial effects on groundwater storage or surface discharge, and severe drought intensifies the stresses affecting water resources.

In support of the national census of water resources, the U.S. Geological Survey (USGS) completed the national brackish groundwater assessment to provide information about brackish groundwater as a potential resource to augment or replace freshwater supplies (Stanton and others, 2017). The objectives of the brackish groundwater assessment were to consolidate available data into a comprehensive database of brackish groundwater resources in the United States and to produce a summary report about the distribution, physical and chemical characteristics, and use of brackish groundwater. This fact sheet summarizes the occurrence of brackish groundwater and factors affecting its usability in the southwestern United States (specifically the Southwest Basins region) reported for the national study. The map below (fig. 1) summarizes the brackish zones for the five largest principal aquifers within the southwestern United States, along with groundwater resources in the remaining part of the region (Reilly and others, 2008).

Sea‐level rise, habitat loss, and potential extirpation of a salt marsh specialist bird in urbanized landscapes

Released August 02, 2018 16:15 EST

2018, Ecology and Evolution

Jordan Rosencranz, Karen M. Thorne, Kevin J. Buffington, John Y. Takekawa, Ryan F. Hechinger, Tara E. Stewart, Richard F. Ambrose, Glen M. MacDonald, Mark A. Holmgren, Jeff A. Crooks, Robert T. Patton, Kevin D. Lafferty

Sea‐level rise (SLR) impacts on intertidal habitat depend on coastal topology, accretion, and constraints from surrounding development. Such habitat changes might affect species like Belding's savannah sparrows (Passerculus sandwichensis beldingi; BSSP), which live in high‐elevation salt marsh in the Southern California Bight. To predict how BSSP habitat might change under various SLR scenarios, we first constructed a suitability model by matching bird observations with elevation. We then mapped current BSSP breeding and foraging habitat at six estuarine sites by applying the elevation‐suitability model to digital elevation models. To estimate changes in digital elevation models under different SLR scenarios, we used a site‐specific, one‐dimensional elevation model (wetland accretion rate model of ecosystem resilience). We then applied our elevation‐suitability model to the projected digital elevation models. The resulting maps suggest that suitable breeding and foraging habitat could decline as increased inundation converts middle‐ and high‐elevation suitable habitat to mudflat and subtidal zones. As a result, the highest SLR scenario predicted that no suitable breeding or foraging habitat would remain at any site by 2100 and 2110. Removing development constraints to facilitate landward migration of high salt marsh, or redistributing dredge spoils to replace submerged habitat, might create future high salt marsh habitat, thereby reducing extirpation risk for BSSP in southern California.

Transport of nitrogen and phosphorus in the Cedar River Basin, Iowa and Minnesota, 2000–15

Released August 02, 2018 15:30 EST

2018, Scientific Investigations Report 2018-5090

Stephen J. Kalkhoff

Nitrate concentrations in the Cedar River in Iowa and Minnesota have increased from an average of less than 1.0 milligram per liter in the early 1900s to more than 5.0 milligrams per liter in the 2000s and have resulted in periodic water-quality impairment of the river. Spatial differences and temporal changes in nitrogen and phosphorus transport in the Cedar River Basin are described for the period from 2000 to 2015. Data used to estimate nitrogen and phosphorus transport were collected by the U.S. Geological Survey as part of six base-flow synoptic studies and by the Minnesota Pollution Control Agency and the Iowa Department of Natural Resources as part of their long-term stream and river monitoring programs. The Cedar River transported an annual average of 53,100 tons of total nitrogen and 2,510 tons of total phosphorus during 2000–15. Three subbasins yielded an annual average of more than 30 pounds per acre (lb/acre) of nitrogen to the Cedar River, whereas two subbasins yielded an annual average of less than 20 lb/acre of nitrogen. The average annual total phosphorus yield from the Little Cedar River subbasin (0.35 lb/acre) was only about 16 percent of the yield from the greatest total phosphorus yielding Lower Cedar River subbasin (more than 1.0 lb/acre). The annual total nitrogen and total phosphorus loads did not change significantly during the study. The relation between annual stream runoff and annual total nitrogen and total phosphorus yields was not spatially uniform across the Cedar River Basin. The Beaver Creek, Black Hawk Creek, and Wolf Creek subbasins yielded the most, and the Main Stem Middle Cedar River, the Lower Cedar River, and the Little Cedar River subbasins yielded the least amount of nitrogen for a given amount of runoff. The Lower Cedar River and Wolf Creek subbasins yielded the most and the West Fork Cedar River and the Little Cedar River subbasins yielded the least phosphorus for a given amount of runoff. The results of this study describe nutrient transport during 2000–15 that can be used to evaluate future progress of nutrient reduction strategies in the Cedar River Basin.

Extinction risk and conservation options for Maui Parrotbill, an endangered Hawaiian honeycreeper

Released August 02, 2018 15:06 EST

2018, Journal of Fish and Wildlife Management

Hanna L. Mounce, Christopher C. Warren, Conor P. McGowan, Eben H. Paxton, J.J. Groombridge

Extinction rates for island birds around the world have been historically high. For forest passerines, the Hawaiian archipelago has suffered some of the highest extinction rates and reintroduction is a conservation tool that can be used to prevent the extinction of some of the remaining endangered species. Population viability analyses can be used to assess risks to vulnerable populations and evaluate the relative benefits of conservation strategies. Here we present a population viability analysis to assess the long-term viability for Maui parrotbill(s) (Kiwikiu) Pseudonestor xanthophrys, a federally endangered passerine on the Hawaiian island of Maui. Contrary to indications from population monitoring, our results indicate Maui parrotbills may be unlikely to persist beyond 25 years. Our modeling suggests female mortality as a primary factor driving this decline. To evaluate and compare management options involving captive rearing and translocation strategies we made a female-only stage-structured, meta-population simulation model. Due to the low reproductive potential of Maui parrotbills in captivity, the number of individuals (~ 20% of the global population) needed to source a reintroduction solely from captive reared birds is unrealistic. A reintroduction strategy that incorporates a minimal contribution from captivity and instead translocates mostly wild individuals was found to be the most feasible management option. Habitat is being restored on leeward east Maui, which may provide more favorable climate and habitat conditions and promote increased reproductive output. Our model provides managers with benchmarks for fecundity and survival needed to ensure reintroduction success, and highlights the importance of establishing a new population in potentially favorable habitat to ensure long-term persistence.

Isolation by distance versus landscape resistance: Understanding dominant patterns of genetic structure in Northern Spotted Owls (Strix occidentalis caurina)

Released August 02, 2018 12:20 EST

2018, PLoS ONE (13) 1-14

Mark P. Miller, Raymond J. Davis, Eric D. Forsman, Thomas D. Mullins, Susan M. Haig

Landscape genetics investigations examine how the availability and configuration of habitat influence genetic structure of plants and animals. We used landscape genetics to evaluate the role that forest connectivity plays in determining genetic structure of the federally-threatened Northern Spotted Owl (Strix occidentalis caurina) using genotypes of 339 Northern Spotted Owls obtained for 10 microsatellite loci. Spatial clustering analyses identified a distinct genetic cluster at the southern extent of the region examined. This cluster could not be linked to landscape connectivity patterns and suggested that post-Pleistocene processes were involved with its development rather than contemporary landscape configuration. We also compared matrices of pairwise inter-individual genetic distances with resistance distances derived from a circuit-theory based framework. Resistance distances were obtained for an idealized raster map that reflected continuous unimpeded dispersal habitat across the landscape along with five empirically-derived raster maps reflecting the 1870’s, 1940’s, 1986, 1994, and 2012. Resistance distances from the idealized map served as surrogates for linear geographic distances. Relative to idealized conditions, resistance distances were ~250% higher in the 1940’s and ~200% higher from 1986 onward. Resistance distances from the 1870’s were ~40% higher than idealized conditions. Inter-individual genetic distances were most highly correlated with resistance distances from the idealized map rather than any of the empirical maps. Two hypotheses explain our results. First, our results may reflect temporal lags between the onset of large-scale habitat alterations and their novel effects on genetic structure in long-lived species such as Northern Spotted Owls. Second, because Northern Spotted Owls disperse over long distances, our results may indicate that forest habitat has never been sufficiently fragmented to the point where connectivity was disrupted. The second hypothesis could indicate that forest management practices mandated by the Northwest Forest Plan succeeded with one of its primary goals. However, our results do not represent a complete portrayal of the status of Northern Spotted Owls given detection of significant population declines and bottlenecks in other studies. Future investigations based on computer simulations may help distinguish between hypotheses.

Volcanic eruptions and threats to respiratory health

Released August 02, 2018 11:48 EST

2018, American Journal of Respiratory and Critical Care Medicine (197) P21-P22

W. Graham Carlos, Jane E. Gross, Shazia Jamil, Charles S. Dela Cruz, David Damby, Elizabeth K. Tam

In early May 2018, Kīlauea volcano became increasingly active, posing an increase in threat to respiratory health. The emission of gases such as sulfur dioxide from Kīlauea produces large amounts of respirable acid particles as the gases react with water vapor and sunlight, resulting in a visible haze called “vog”. Additionally, the lava lake at Kīlauea’s summit crater has fallen, leading to explosions of “ash” that have reached as high up as 30,000 feet above sea level. Finally, lava entering the Pacific Ocean boils sea water to dryness, creating thick clouds of “laze” that is filled with hydrochloric acid and tiny shards of glass. Depending on your location and wind direction and speed, vog, ash, and laze can reach hazardous levels of air pollution that are toxic to humans. This fact sheet serves to inform you of potential adverse health effects following exposure to these airborne products of volcanic activity. This outdoor air quality issue is relevant to other locations worldwide at risk for volcanic activity.

Riparian defoliation by the invasive green alder sawfly influences terrestrial prey subsidies to salmon streams

Released August 02, 2018 11:41 EST

2018, Ecology of Freshwater Fish

David A. Roon, Mark S. Wipfli, James J. Kruse

Invasive species in riparian forests are unique as their effects can transcend ecosystem boundaries via stream‐riparian linkages. The green alder sawfly (Monsoma pulveratum) is an invasive wasp whose larvae are defoliating riparian thin‐leaf alder (Alnus tenuifolia) stands across southcentral Alaska. To test the hypothesis that riparian defoliation by this invasive sawfly negatively affects the flow of terrestrial prey resources to stream fishes, we sampled terrestrial invertebrates on riparian alder foliage, their subsidies to streams and their consumption by juvenile coho salmon (Oncorhynchus kisutch). Invasive sawflies altered the composition of terrestrial invertebrates on riparian alder foliage and as terrestrial prey subsidies to streams. Community analyses supported these findings revealing that invasive sawflies shifted the community structure of terrestrial invertebrates between seasons and levels of energy flow (riparian foliage, streams and fish). Invasive sawfly biomass peaked mid‐summer, altering the timing and magnitude of terrestrial prey subsidies to streams. Contrary to our hypothesis, invasive sawflies had no effect on the biomass of native taxa on riparian alder foliage, as terrestrial prey subsidies, or in juvenile coho salmon diets. Juvenile coho salmon consumed invasive sawflies when most abundant, but relied more on other prey types selecting against sawflies relative to their availability. Although we did not find effects of invasive sawflies extending to juvenile coho salmon in this study, these results could change as the distribution of invasive sawflies expands or as defoliation intensifies. Nevertheless, riparian defoliation by these invasive sawflies is likely having other ecological effects that merits further investigation.

Timescales of magmatic differentiation from alkali basalt to trachyte within the Harrat Rahat volcanic field, Kingdom of Saudi Arabia

Released August 02, 2018 11:32 EST

2018, Contributions to Mineralogy and Petrology (173) 1-17

Mark Stelten, Drew Downs, Hannah Dietterich, Gail A. Mahood, Andrew T. Calvert, Thomas W. Sisson, Hani Zahran, Jamal Shawali

A fundamental goal of igneous petrology is to quantify the duration of time required to produce evolved magmas following influx of basalt into the crust. However, in many cases, complex field relations and/or the presence of a long-lived magmatic system make it difficult to assess how basaltic inputs relate to more evolved magmas, therefore, precluding calculation of meaningful timescales. Here, we present field relations, geochemistry, 40Ar/39Ar ages, and 36Cl ages for volcanic rocks from the Harrat Rahat volcanic field, Saudi Arabia. These data document a systematic and repeated temporal progression from alkali basalt to trachyte for the youngest eruptives. From ~ 150 to ~ 17 ka the following eruptive sequence occurred four times: (1) alkali basalt, (2) hawaiite, mugearite, or benmoreite, and (3) trachyte. We interpret each eruptive sequence to result from injection of basalt into the crust, and its subsequent differentiation and eruption of progressively evolved magmas. We use the interval time between successive eruptions within a given sequence to calculate the duration of time required to produce trachyte from alkali basalt. Differentiation from alkali basalt to intermediate compositions (hawaiite, mugearite, benmoreite) took ≤ 2 kyr on average. Differentiation from intermediate compositions to trachyte took a maximum of 6.6 ± 3.5 to 22.5 ± 1.6 kyr. Thus, the total duration of differentiation was ~ 9 to ~ 25 kyr. Timescales presented here are insensitive to processes evoked to drive differentiation because they are based solely on the ages and compositions of eruptive products from a system characterized by a simple, repeated differentiation sequence.

Geologic map of the Hayfield quadrangle, Frederick County, Virginia

Released August 01, 2018 16:45 EST

2018, Scientific Investigations Map 3407

Daniel H. Doctor, Ronald A. Parker

The Hayfield 7.5-minute quadrangle is located within the Valley and Ridge physiographic province of northern Virginia. The quadrangle includes the topographical lowland area of the northern Great Valley to the southeast, the narrow ridge of Little North Mountain along the western edge of the Great Valley, and the broad region of elongated valleys and ridges east of Little North Mountain. The most prominent physiographic feature within the quadrangle is Great North Mountain, which extends across the northwestern portion of the quadrangle. All exposed bedrock units are Paleozoic sedimentary rocks ranging from Middle Cambrian to Late Devonian, approximately 513 to 359 Ma. The clastic and carbonate sedimentary strata in the quadrangle reflect nearshore and offshore marine and deltaic depositional environments. The deposits indicate minor sea level transgression and regression cycles along a passive continental margin during the Late Cambrian to Middle Ordovician, and major sea level changes resulting from tectonic uplift during the Late Ordovician Taconian orogeny and the Middle to Late Devonian Acadian orogeny. Compressive forces caused by the continental collision during the Paleozoic Alleghanian orogeny resulted in folding and faulting of the sedimentary rock strata, with northwestward tectonic transport. The North Mountain fault zone, spanning across the southeastern part of the quadrangle, forms the western border of the Great Valley in northern Virginia and is a series of northeast-trending thrust faults with multiple splays that separate the Silurian and Devonian shales, siltstones, and sandstones from the Cambrian and Ordovician carbonate rocks and shales. Topographic ridges in the quadrangle are primarily held up by sandstones and orthoquartzites that are relatively resistant to erosion. Surficial materials include unconsolidated alluvium, colluvium, debris flow, and terrace deposits that are assumed to be of Quaternary age. Alluvium was mapped along the larger streams; locally, some low alluvial terraces exist but have not been broken out within this unit. Debris flow deposits were mapped where recognized in the lidar-derived topographic imagery on the flanks of Great North Mountain. Colluvium (not mapped separately) covers most of the steeper slopes and fills the bottoms of many of the mountain hollows, and is composed mainly of sandstone boulders and cobbles, and fragments of chert.

Tritium deposition in precipitation in the United States, 1953–2012

Released August 01, 2018 15:32 EST

2018, Scientific Investigations Report 2018-5086

Robert L. Michel, Bryant C. Jurgens, Megan B. Young

Tritium is a radioactive isotope of hydrogen (half-life is equal to 12.32 years). Since it is part of the water molecule, tritium can be used to track and date groundwater and surface water when the history of tritium in precipitation and recharge is known. To facilitate that effort, tritium concentrations in precipitation were reconstructed from measurements and correlations for 10 precipitation stations in the continental United States. Using these data, and other data sets and correlations, estimates of tritium concentrations in precipitation from 1953 through 2012 and total tritium deposition from 1953 through 1983 were derived for 2 degrees latitude by 5 degrees longitude quadrangles of the continental United States. For August 1953 through December 1987 correlations were derived from the data of the Ottawa, Canada, station; for estimates after 1987, the Vienna, Austria, station was used. For quadrangles where no precipitation station records are available from measurements or correlations, concentrations were interpolated. The International Atomic Energy Agency has proposed that a correlation with the Vienna, Austria, station, which has been in operation since 1960, be used instead of the Ottawa, Canada, station for the period after 1987. Linear correlations calculated for all stations with the Vienna data are reported. Correlations also have been calculated for each latitude-longitude quadrangle using the estimated concentrations and the measured Vienna data for 1960–87. Because the Vienna, Austria, station is on a different continent, and not subject to the same seasonal weather patterns that affect North American stations, a correlation was obtained for each month individually. This reflects the fact that the North American stations were strongly affected by the input of low-tritium moisture from the south during the summer. The correlated station values were then used with measured Vienna data to obtain estimates of tritium concentrations in precipitation for the period 1988–2012 at each precipitation station and latitude-longitude quadrangles. This approach has two major advantages: (1) it blends the Ottawa correlation with the Vienna correlation to cover the period 1953 to present, and (2) it yields correlation coefficients for each quadrangle that can be used in future years when more data become available from the Vienna, Austria, station. The data, the estimated tritium concentrations derived from the correlations, and the correlation coefficients are provided as spreadsheets and associated comma delimited files in a data release that accompanies this report.

Limits to ponderosa pine regeneration following large high-severity forest fires in the United States Southwest

Released August 01, 2018 14:57 EST

2018, Fire Ecology (14) 143-163

Collin Haffey, Thomas D. Sisk, Craig D. Allen, Andrea E. Thode, Ellis Margolis

High-severity fires in dry conifer forests of the United States Southwest have created large (>1000 ha) treeless areas that are unprecedented in the regional historical record. These fires have reset extensive portions of Southwestern ponderosa pine (Pinus ponderosa Lawson & C. Lawson var. scopulorum Engelm.) forest landscapes. At least two recovery options following high-severity fire are emerging. One option is for post-fire successional pathways to move toward a return to the pre-fire forest type. Alternatively, an area may transition to persistent non-forested ecosystems. We studied regeneration patterns of ponderosa pine following eight fires in Arizona and New Mexico, USA, that burned in dry conifer forests dominated by ponderosa pine during a recent 18-year regional drought period, 1996 to 2013. Our a priori hypotheses were: 1) the most xeric areas within these severely burned dry conifer forests are least likely to regenerate to the pre-fire forest type due to persistent post-fire moisture stress; and 2) areas farther away from conifer seed sources have a lower likelihood of regeneration, even if these areas are climatically favorable for post-fire ponderosa pine establishment. We evaluated our hypotheses using empirical data and generalized linear mixed-effects models. We found that low-elevation, xeric sites are more limiting to conifer regeneration than higher-elevation mesic sites. Areas >150 m from a seed source are much less likely to have ponderosa pine regeneration. Spatial interpolations of modeled post-fire regeneration of ponderosa pine across the study landscapes indicate expansive areas with low likelihood of pine regeneration following high-severity fire. We discuss multiple post-fire successional pathways following high-severity fire, including potentially stable transitions to non-forest vegetation types that may represent long-term type conversions. These findings regarding landscape changes in Southwest forests in response to fires and post-fire regeneration patterns during early-stage climate warming contribute to the development of better-informed ecosystem management strategies for forest adaptation or mitigation under projected hotter droughts in this region.

The influence of nutrients from carcasses of sea lamprey (Petromyzon marinus) on larval growth and spawner abundance

Released August 01, 2018 14:45 EST

2018, Fishery Bulletin (116) 142-152

Daniel M. Weaver, Stephen M. Coghlan Jr., Joseph D. Zydlewski

Migrations of anadromous sea lamprey (Petromyzon marinus) from marine ecosystems serve as vectors of nutrients into freshwater food webs. Larval sea lamprey reside in streams for 6–8 years as deposit feeders before metamorphosing into juveniles and migrating to the ocean. Previous work has shown that carcass nutrients, which result from the death of adult lamprey after spawning, increase stream productivity and are consumed by larvae. This may increase larval growth rates and enhance earlier metamorphosis. We examined the sensitivity of life-history parameters and influence of nutrients from carcasses of sea lamprey on the age and growth of larval conspecifics with a deterministic stock-recruitment model. We hypothesized that variability in growth among larval populations is productivity mediated and we compared modeled populations in which larvae receive added growth benefits from carcass nutrients with populations that do not. The results of our simulation indicate that increases in larval growth and lower age at metamorphosis over time lead to an increase in spawner abundance. Increased growth rates may also improve fitness and bolster subsequent spawning stocks. Our research characterized 2 potential ecosystem states, one in which larval sea lamprey benefit from adult conspecifics and another in which the larvae do not.

Influencia de factores ambientales y biométricos en la capacidad de nado del barbo ibérico (Luciobarbus bocagei Steindachner, 1864), un ciprínido potamódromo endémico de la Península Ibérica

Released August 01, 2018 13:57 EST

2018, Limnetica (37) 251-265

Jorge Ruiz-Legazpi, F.J. Sanz-Ronda, F.J. Bravo-Cordoba, J.F. Fuentes-Perez, Theodore R. Castro-Santos

El presente trabajo analiza la capacidad voluntaria de nado del barbo ibérico (Luciobarbus bocagei Steindachner, 1864) en un canal abierto durante su época de migración, relacionándola con factores ambientales y biométricos. La temperatura del agua, la velocidad de flujo y la longitud del pez fueron los factores de mayor importancia que condicionaron la velocidad de nado de los barbos y su tiempo de fatiga. Dentro del rango de valores estudiado, el barbo ibérico pudo mantener velocidades de nado en sprint (> 15 BL/s) durante 3-10 s, y de 17-117 s en el modo de natación prolongada (7-15 BL/s). Los resultados aportados pueden ser empleados como una herramienta útil para la gestión de sus poblaciones, principalmente para el diseño de pasos para peces.

This paper analyzes the volitional swimming capacity of the Iberian barbel (Luciobarbus bocagei Steindachner, 1864) in an open flume during its migration period, in relation to environmental and biometric factors. Water temperature, flow velocity and fish length were the most important factors which affected the swimming speed of barbels and their fatigue time. Within the range of values studied, the Iberian barbel was able to maintain sprint swim speeds (> 15 BL/s) for 3-10 s, and 17-117 s in prolonged swim mode (7-15 BL/s). The results can be used as a tool for the management of barbel populations, mainly in the design of fishways.

Gas emissions, tars, and secondary minerals at the Ruth Mullins and Tiptop coal mine fires

Released August 01, 2018 13:33 EST

2018, International Journal of Coal Geology (195) 304-316

Jennifer M. K. O'Keefe, Erika R. Neace, Maxwell L. Hammond III, James C. Hower, Mark A. Engle, Joseph A. East, Nicholas J. Geboy, Ricardo A. Olea, Kevin R. Henke, Gregory C. Copley, Edward W. Lemley, Rachel S. Hatch Nally, Antonia E. Hansen, Allison R. Richardson, Anne B. Satterwhite, Glenn B. Stracher, Larry F. Radke, Charles Smeltzer, Christopher Romanek, Donald R. Blake, Paul A. Schroeder, Stephen D. Emsbo-Mattingly, Scott A. Stout

Both the Tiptop and Ruth Mullins coal fires, Kentucky, were reinvestigated in 2009 and 2010. The Tiptop fire was not as active in 2009 and may have been on the path to burning out at the time of the 2009 visit. The Ruth Mullins coal mine fire, Perry County, Kentucky, has been the subject of several field investigations, including November 2009–February 2010 investigations in which we measured gas emissions, collected minerals and tars, and characterized the nature of the fire. Vents exhibiting the greatest gas flux (>100,000 mg/s/m2) are those with the largest amount of condensate minerals and tars. Vents with moderate gas flux (10,000–100,000 mg/s/m2) are less likely to contain condensate minerals, but are collocated with tars, and vents with the lowest flux (<10,000 mg/s/m2) generally lack both minerals and tars. Aliphatic hydrocarbons present in the gases include C1-C9 compounds, and aromatics include BTEX compounds. Diffuse-CO2emissions are concentrated along the fracture zones overlying abandoned mine works. The area of peak diffuse flux corresponds to the trend of the collapsed portal that forms vent 5. The greatest vent emissions were also recorded at vent 5. The snow-melt zone mapped in January 2010 overlies the areas of peak diffuse-CO2 emissions measured in November; together they delineate the zone of active combustion. Comparison of greenhouse gas emissions from the two sources shows that vent emissions exceed diffuse emissions. The highly fractured, quartz-cemented roof rock funnels the majority of emissions toward the vents. Significant decreases are seen in estimates of yearly greenhouse emissions based on data gathered from November 2009 to February 2010, with estimates from November significantly exceeding any previously published estimates. For example, September 2009 estimates from vent 3 alone indicated that 19 ± 7.5 T CO2/yr were emitted while the November 2009 estimates were 1800 ± 690 T/yr. Barometric pressure was lower in November than September. This implies that there are many factors influencing the seasonal variations in fire emissions and that more frequent monitoring will be necessary to derive accurate estimates of coal fires' contribution to the carbon budget.

Selective occupancy of a persistent yet variable coastal river plume by two seabird species

Released August 01, 2018 12:31 EST

2018, Marine Ecology Progress Series (594) 245-261

Elizabeth M. Phillips, John K. Horne, Josh Adams, Jeannette E. Zamon

Advances in telemetry and modeling of physical processes expand opportunities to assess relationships between marine predators and their dynamic habitat. The Columbia River plume (CRP) attracts sooty shearwaters Ardenna grisea and common murres Uria aalge, but how seabirds respond to variability in plume waters is unknown. We characterized seabird distributions in relation to hourly, daily, monthly, and seasonal variation in CRP location and surface area by attaching satellite telemetry tags to shearwaters in 2008 and 2009, and to murres in 2012 and 2013. We matched seabird locations to surface salinity from a high-resolution hydrodynamic model of the CRP and adjacent waters. Utilization distributions indicated high-use areas north of the Columbia River mouth and in continental shelf waters. Shearwater and murre occupancy of tidal (<21 psu), recirculating (21-26 psu), and boundary (26-31 psu) plume waters was on average 31% greater than expected and positively correlated with CRP surface area. Seabird latitude was positively correlated with latitude of the geographic center of the CRP, indicating that birds move in phase with the plume. We detected a threshold response of seabirds to plume size, and birds were closer to the convergent CRP boundary (28 psu isohaline) after a surface area threshold between 1500 and 4000 km2 was exceeded. We conclude that shearwaters and murres selectively occupy and track plume waters, particularly dynamic boundary waters where foraging opportunities may be enhanced by increases in surface area and associated biophysical coupling that aggregates zooplankton and attracts prey fishes.

Salinity tolerance among three freshwater mussels (Bivalvia: Unionidae) from Gulf Coastal Plain drainages

Released August 01, 2018 11:45 EST

2018, Florida Scientist (81) 61-69

Nathan A. Johnson, Pam Schofield, James D. Williams, James D. Austin

An important physiological constraint influencing distributions of coastal freshwater organisms is their tolerance for saline conditions. We experimentally evaluated salinity tolerance for three freshwater mussel species (Utterbackia imbecillis, Elliptio jayensis, and Glebula rotundata). Mussels were transferred abruptly from well water to one of five treatments (0 [control], 6, 12, 18 or 24 parts per thousand [ppt]). Utterbackia imbecillis survived on average about 2 days at treatments 6 ppt, while Elliptio jayensis survived slightly longer (about 4 days). Glebula rotundata was most tolerant to salinity, surviving as well at 6 and 12 ppt as it did in the control. Additionally, G. rotundata survived at higher salinities (18 and 24 ppt) for an average of 7–8 days. To our knowledge, this is the highest salinity tolerance ever reported for a unionid. The salinity tolerance of U. imbecillis may be influenced by its inability to completely seal its valves. The variation we found in salinity tolerance of these species corresponds with their distributions in the Gulf Coastal Plain drainages: U. imbecillis and E. jayensis are primarily found in strictly freshwater habitats whereas G. rotundata inhabits lower reaches of rivers closer to the coast. Stressors such as increased frequency and intensity of storms, sea level rise, drought, low flows, fossil fuel extraction, and municipal water withdrawals, among others, may increase salinities in freshwater ecosystems, potentially stressing mussels such as U. imbecillis and E. jayensis with low salinity tolerance.

Broad‐scale occurrence of a subsidized avian predator: reducing impacts of ravens on sage‐grouse and other sensitive prey

Released August 01, 2018 11:14 EST

2018, Journal of Applied Ecology

Shawn T. O'Neil, Peter S. Coates, Brianne E. Brussee, Pat J. Jackson, Kristy B. Howe, Ann M. Moser, Lee J. Foster, David J. Delehanty

Expanding human enterprise across remote environments impacts numerous wildlife species. Anthropogenic resources provide subsidies for generalist predators that can lead to cascading effects on prey species at lower trophic levels. A fundamental challenge for applied ecologists is to disentangle natural and anthropogenic influences on species occurrence, and subsequently develop spatially explicit models to help inform management and conservation decisions.

Using Bayesian hierarchical occupancy models, we mapped the broad‐scale occurrence of common ravens Corvus corax as a function of natural and anthropogenic landscape covariates using >15,000 point count surveys performed during 2007–2016 within the Great Basin region, USA. Raven abundance and distribution is substantially increasing across the American west due to unintended anthropogenic resource subsidies. Importantly, ravens prey on eggs and chicks of numerous species including greater sage‐grouse Centrocercus urophasianus, an indicator species whose decline is at the centre of national conservation strategies and land use policies.Anthropogenic factors that contributed to greater raven occurrence were: increased road density, presence of transmission lines, agricultural activity, and presence of roadside rest areas. Natural landscape characteristics included lower elevations with greener vegetation (NDVI), greater stream and habitat edge densities, and lower percentages of big sagebrush A. tridentata spp.

Interactions between anthropogenic sources of nesting substrate and food subsidies suggested that raven occurrence increased multiplicatively when these resource subsidies co‐occurred. Overall, the average probability of raven occurrence estimated within sagebrush ecosystems of the study area was ~0.83.

Synthesis and applications. We demonstrate how anthropogenic factors can be disentangled from natural effects when making spatially‐explicit predictions of subsidized predators occurring across expansive landscapes. This approach can guide management decisions where subsidized predators overlap sensitive prey habitats. For example, we identify areas where elevated raven occurrence coincides with breeding sage‐grouse concentration areas and appears to be largely driven by anthropogenic factors. Management applications could focus on reducing raven access to anthropogenic subsidies in these areas, while prioritizing habitat improvements for sage‐grouse elsewhere. Our approach is applicable to other species where widespread survey data are available.

Complex bedding geometry in the upper portion of Aeolis Mons, Gale crater, Mars

Released August 01, 2018 10:56 EST

2018, Icarus (314) 246-264

Ryan Anderson, Lauren Edgar, David M. Rubin, Kevin W. Lewis, Claire Newman

The Upper formation of Aeolis Mons in Gale crater exhibits curvilinear bedding patterns on the surfaces of several erosional benches that have been interpreted as cross-bedding. We use High Resolution Imaging Science Experiment (HiRISE) stereo topography to test this hypothesis by measuring the bedding geometry within these benches. The bedding geometry is consistent with aeolian cross-beds: measured dips rarely exceed the angle of repose, and the distribution of dip azimuths is non-random, allowing dune morphology and paleo-transport directions to be inferred using computer models of bedforms. The inferred dune type and transport direction vary between the benches of the Upper formation, indicating that the benches are separated by sufficient time for the wind regime to change. The paleo-wind directions derived from bedding geometry measurements differ from modern wind modeling results, suggesting that the conditions during deposition of the Upper formation were unlike modern conditions. The concentric bedding patterns in some locations indicate that the rate of deposition approached the rate of bedform migration. The evidence for lithified hundred-meter-scale dunes in the Upper formation of Aeolis Mons indicates that the area was a sediment sink at the time of formation, and any hypothesis for the formation of Aeolis Mons must be compatible with these results. We present one possible sequence of events for the formation of Aeolis Mons.

Hydrothermal discharge from the El Tatio basin, Atacama, Chile

Released August 01, 2018 10:54 EST

2018, Journal of Volcanology and Geothermal Research

Carolina Munoz-Saez, Michael Manga, Shaul Hurwitz

El Tatio in northern Chile is one of the best-studied geothermal fields in South America. However, there remain open questions about the mass and energy budgets, water recharge rates and residence time in the subsurface, origin of dissolved solutes, and processes affecting the phase and chemical composition of groundwater and surface water. We measured and sampled surface manifestations of the geothermal system (geysers perpetual spouters, mud pools/volcanoes, and non-eruptive hot springs) and meteoric water. From the isotopic composition we infer that the thermal water has a meteoric origin that is different from the composition of local meteoric water. The absence of detectable tritium in thermal waters indicates that most of the recharge occurred pre-1950. Boiling and steam separation from the deep reservoir appear to be the main subsurface processes affecting the thermal fluids. A large amount of heat is lost to the atmosphere by evaporation from surface water and by steam emitted from erupting geysers. Using the chloride inventory method, we estimate thermal water discharge to be 218 to 234 L/s, and the advective heat flow to be 120 to 170 MW.

Next‐generation conservation genetics and biodiversity monitoring

Released August 01, 2018 10:47 EST

2018, Evolutionary Applications (11) 1029-1034

Margaret E. Hunter, Sean M. Hoban, Michael W. Bruford, Gernot Segelbacher, Louis Bernatchez

This special issue of Evolutionary Applications consists of 10 publications investigating the use of next‐generation tools and techniques in population genetic analyses and biodiversity assessment. The special issue stems from a 2016 Next Generation Genetic Monitoring Workshop, hosted by the National Institute for Mathematical and Biological Synthesis (NIMBioS) in Tennessee, USA. The improved accessibility of next‐generation sequencing platforms has allowed molecular ecologists to rapidly produce large amounts of data. However, with the increased availability of new genomic markers and mathematical techniques, care is needed in selecting appropriate study designs, interpreting results in light of conservation concerns, and determining appropriate management actions. This special issue identifies key attributes of successful genetic data analyses in biodiversity evaluation and suggests ways to improve analyses and their application in current population and conservation genetics research.

Structural-group quantitation by CP/MAS 13C NMR measurements of dissolved organic matter from natural waters

Released August 01, 2018 08:59 EST

2002, Book chapter, Humic substances: Versatile components of plants, soils and water

R. L. Wershaw, George R. Aiken, J. A. Leenheer, J. Tregellas

G. Davis, E.A. Ghabbour, editor(s)

No abstract available. 

Flow hydraulics and mixing characteristics in and downstream from Brandon Road Lock, Joliet, Illinois

Released July 31, 2018 15:30 EST

2018, Scientific Investigations Report 2018-5094

Frank L. Engel, P. Ryan Jackson, Elizabeth A. Murphy

The Brandon Road Lock and Dam on the Des Plaines River near Joliet, Illinois, has been identified for potential implementation of aquatic nuisance species (ANS) control measures. To provide additional information concerning the flow hydraulics and mixing characteristics of the lock and downstream approach channel, the U.S. Geological Survey performed a detailed study of the site between December 2014 and October 2015, which included the collection and analysis of bathymetric, hydrodynamic, and dye tracer data. Synthesis of these data allowed a characterization of the site for future use in feasibility studies of potential ANS control technologies. The results of this study show a highly dynamic system driven primarily by lock operations but influenced by channel characteristics, industrial withdrawals, and meteorological forcing. Lock operation produces rapidly varying flows in the downstream approach channel, including transient oscillations that produce bidirectional flows. When the lock is not in operation, flows in the approach channel are primarily driven by leakage and wind forcing. Uniform concentrations of dissolved constituents in the lock chamber can be achieved by injection of the constituent into the existing lock filling and emptying system; however, valve and gate leakage can inhibit the mixing at the downstream end of the lock and substantially affects the ability to maintain a treated lock chamber at a uniform target concentration at tailwater level. Proper understanding of these hydraulic factors should be accounted for if the lock is to be used to deliver any dissolved constituent or operated in a way to prevent upstream passage of floating ANS. Moreover, extremely variable flow conditions including bidirectional flows and upstream return flows must be considered when implementing any ANS control technologies in the approach channel.

What can trees tell us about the air we breathe at home?

Released July 31, 2018 13:32 EST

2018, Science Journal for Kids (July 2018)

Jordan L. Wilson, V.A. Samaranayake, Matthew A. Limmer, Joel Burken

The air in houses can be affected by bad stuff, called contaminants. Sometimes harmful chemicals enter the air in buildings from nearby contaminated soil and groundwater through cracks or gaps in the foundation – a process known as vapor intrusion. This poses some risk to our health because we spend so much of our time indoors. Currently it’s difficult and expensive to figure out if vapor intrusion is happening. That’s why we wanted to see if trees can serve as indicators for vapor intrusion. We collected samples from 109 trees in a contaminated area in a Nebraska town and analyzed them for tetrachloroethene (PCE), a chemical used mostly as a cleaner and to make other chemicals. When comparing our results with the data the U.S. Environmental Protection Agency (EPA) had collected, we found that trees are good indicators of vapor intrusion.

Simulation of zones of groundwater contribution to wells south of the Naval Weapons Industrial Reserve Plant in Bethpage, New York

Released July 31, 2018 12:00 EST

2018, Scientific Investigations Report 2017-5161

Paul E. Misut

A steady-state three-dimensional groundwater-flow model that simulates present conditions was coupled with the particle-tracking program MODPATH to delineate zones of contribution to wells pumping from the Magothy aquifer near a chlorinated volatile organic compound (VOC) plume. This modeling was part of a study by the U.S. Geological Survey in cooperation with the Naval Facilities Engineering Command to delineate groundwater near the Naval Weapons Industrial Reserve Plant in Bethpage, New York. Because rates of advection within the coarse-grained sediments typically exceed 0.1 foot per day, transport by dispersion and (or) diffusion was assumed to be negligible. Resulting zones of contribution are complex shapes, influenced by hydrogeologic features including confining beds and a basal gravel zone, and the interplay of nearby hydrologic stresses. The use of two particle tracking techniques identified zones of contribution to wells. Particles are backtracked from pumping well screens, and particles are forward tracked from the location of a VOC plume, as defined by surfaces of equal total VOC concentration. During any period of 5 years or less, about 1 to 3 percent of particles backtracked from pumping wells within a focus area intersected the 5-part per billion (ppb) VOC plume shell, indicating that the vast majority of particles were not sourced from the plume. During 5 years or less, none of the particles backtracked from pumping wells intersected the 50-ppb VOC plume shell. Forward-tracking techniques identified the fate of water within the VOC plume after 5 years as it moves toward ultimate well capture and (or) discharge to model constant head and drain boundaries. Out of 4,813 forward tracked particles started within the 50-ppb VOC plume shell, 1 forward-tracked particle was captured by well ANY8480. Out of 22,958 forward tracked particles started within the 5-ppb VOC plume shell, 100 were captured by production wells (less than 1 percent). The subset of forward pathlines that represent well plume capture are similar in number and shape to those of backtracked pathlines.

Model simulations were conducted to assess uncertainties and improve understanding of how variability in hydraulic properties, pumpage rates, and maximum particle traveltime affect delineation of zones of contribution. By use of driller’s’ logs, a transitional probability approach generated nine alternative realizations of heterogeneity within the Magothy aquifer to assess uncertainty in model representation. Fine-grained sediments with low hydraulic conductivity were realized as laterally discontinuous, thickening towards the south, and comprising about 27 percent of the total aquifer volume within the transitional probability subgrid. Model simulations with alternative pumpage rates, porosity terms, and alternative maximum particle traveltime were also used to demonstrate how the size and shape of zones of contribution may vary.

Snowmelt timing regulates community composition, phenology, and physiological performance of alpine plants

Released July 31, 2018 11:42 EST

2018, Frontiers in Plant Science (9) 1-13

Daniel E. Winkler, Ramona J. Butz, Matthew J. Germino, Keith Reinhardt, Lara M. Kueppers

The spatial patterning of alpine plant communities is strongly influenced by the variation in physical factors such as temperature and moisture, which are strongly affected by snow depth and snowmelt patterns. Earlier snowmelt timing and greater soil-moisture limitations may favor wide-ranging species adapted to a broader set of ecohydrological conditions than alpine-restricted species. We asked how plant community composition, phenology, plant water relations, and photosynthetic gas exchange of alpine-restricted and wide-ranging species differ in their responses to a ca. 40-day snowmelt gradient in the Colorado Rocky Mountains (Lewisia pygmaeaSibbaldia procumbens, and Hymenoxys grandiflora were alpine-restricted and Artemisia scopulorumCarex rupestris, and Geum rossii were wide-ranging species). As hypothesized, species richness and foliar cover increased with earlier snowmelt, due to a greater abundance of wide-ranging species present in earlier melting plots. Flowering initiation occurred earlier with earlier snowmelt for 12 out of 19 species analyzed, while flowering duration was shortened with later snowmelt for six species (all but one were wide-ranging species). We observed >50% declines in net photosynthesis from July to September as soil moisture and plant water potentials declined. Early-season stomatal conductance was higher in wide-ranging species, indicating a more competitive strategy for water acquisition when soil moisture is high. Even so, there were no associated differences in photosynthesis or transpiration, suggesting no strong differences between these groups in physiology. Our findings reveal that plant species with different ranges (alpine-restricted vs. wide-ranging) could have differential phenological and physiological responses to snowmelt timing and associated soil moisture dry-down, and that alpine-restricted species’ performance is more sensitive to snowmelt. As a result, alpine-restricted species may serve as better indicator species than their wide-ranging heterospecifics. Overall, alpine community composition and peak % cover are strongly structured by spatio-temporal patterns in snowmelt timing. Thus, near-term, community-wide changes (or variation) in phenology and physiology in response to shifts in snowmelt timing or rates of soil dry down are likely to be contingent on the legacy of past climate on community structure.

Understanding the effect of salinity tolerance on cyanobacteria associated with a harmful algal bloom in Lake Okeechobee, Florida

Released July 31, 2018 10:45 EST

2018, Scientific Investigations Report 2018-5092

Barry H. Rosen, Keith A. Loftin, Jennifer L. Graham, Katherine N. Stahlhut, James M. Riley, Brett D. Johnston, Sarena Senegal

In an effort to simulate the survival of cyanobacteria as
they are transported from Lake Okeechobee to the estuarine
habitats that receive waters from the lake, a bioassay
encompassing a range of salinities was performed. An overall
decline in cyanobacteria health in salinity treatments greater
than 18 practical salinity units (psu) was indicated by loss of
cell membrane integrity based on SYTOX® Green staining,
but this loss varied by the kind of cyanobacteria present.
Microcystis aeruginosa was tolerant of salinities up to 18 psu;
however, higher salinities caused leaking of microcystin from
the cells. Dolichospermum circinale, another common bloomformer
in this system, did not tolerate salinities greater than
7.5 psu. Stimulation of mucilage production was observed and
is likely a mechanism used by both species to protect organism
viability. At 7.5 psu, microcystin increased relative to
chlorophyll-a, providing some evidence of biosynthesis when
M. aeruginosa is exposed to this salinity. This study indicates
that as freshwater cyanobacteria are transported to brackish
and marine waters, there will be a loss of membrane integrity
which will lead to the release of cellular microcystin into the
surrounding waterbody. Additional research would be needed
to determine the exact effect of salinity on this relationship.

Tilt Trivia: A free multiplayer app to learn geoscience concepts and definitions

Released July 31, 2018 09:21 EST

2018, Seismological Research Letters

Debi Kilb, Alan Yang, Nathan Garrett, Kristine Pankow, Justin L. Rubinstein, Lisa Linville

Today’s technology is opening up new ways to learn. Here, we introduce Tilt Trivia, a suite of quiz‐style, multiplayer games for use on mobile devices and tablets (Android or Apple) to help students learn simple definitions and facts. This mobile device game was built using the Unity engine and has a multiplayer functionality that runs seamlessly, all day, every day. A single game consists of 6–10 questions that are selected at random from a base suite of 13–33 questions. A single Tilt Trivia game takes 3–7 min to complete and allows up to five players to play simultaneously in the same game space. To begin, players select a topical avatar to represent them in the game. While in the competitive playing field, players are presented with a question and then they simply tilt their tablets until their avatar rests on the correct answer marker (i.e., true or false). Because the playing field is constantly tilting, keeping your avatar on the correct answer requires a continual counter‐tilting motion of the tablet to maintain your position within the game. A countdown timer is incorporated requiring players to answer the questions as quickly as possible. At the end of the game, a leaderboard displays the players’ scores and rankings, a metric that motivates repeat play. Players have the option of jostling other players off of the correct answer in the hopes of netting the highest score. The game is configurable to any topic and currently there are games for eight different topics (see Data and Resources).

Effectiveness of a fish ladder for two Neotropical migratory species in the Paraná River

Released July 31, 2018 09:15 EST

2018, Marine and Freshwater Research

Carola Gutfreund, Sergio Makrakis, Theodore R. Castro-Santos, Leandro Celestino, João Henrique Pinheiro Dias, Maristela Cavicchioli Makrakis

We evaluated fish ladder effectiveness at Porto Primavera Dam in the Upper Paraná River, for two Neotropical migratory fish species. Overall, 564 fish (448 Megaleporinus obtusidens and 116 M. piavussu) were PIT-tagged, released in upstream and downstream areas (on the left and right banks), and monitored continuously for 4 years. The fish performed two-way movements through the fish ladder, ascending from the tailrace and descending from the forebay. We registered 46 M. obtusidens (10.3%) and only 3 M. piavussu(2.6%) from the fish ladder, therefore all analyses were focused on M. obstusidens. Entry proportion ranged from 0 to 48.1% depending on release site and was greatest for fish released downstream near the fish ladder entrance. Entry times ranged from 3.0 to 384.0 days, and median times were 32.9 and 25.8 days for downstream and upstream, respectively. Of fish that entered the fish ladder, passage percentages were 80% for fish release downstream and 100% for fish released upstream, and median transit time was 0.7 and 0.9 hours, respectively. Results suggest that if guidance and entry conditions can be improved, this fish ladder design holds promise as an effective solution for providing passage in both directions.

SWB Version 2.0—A soil-water-balance code for estimating net infiltration and other water-budget components

Released July 30, 2018 14:00 EST

2018, Techniques and Methods 6-A59

Stephen M. Westenbroek, John A. Engott, Victor A. Kelson, Randall J. Hunt

The U.S. Geological Survey’s Soil-Water-Balance (SWB) code was developed as a tool to estimate distribution and timing of net infiltration out of the root zone by means of an approach that uses readily available data and minimizes user effort required to begin a SWB application. SWB calculates other components of the water balance, including soil moisture, reference and actual evapotranspiration, snowfall, snowmelt, canopy interception, and crop-water demand. SWB is based on a modified Thornthwaite-Mather soil-water-balance approach, with components of the soil-water balance calculated at a daily time step. Net-infiltration calculations are computed by means of a rectangular grid of computational elements, which allows the calculated infiltration rates to be imported into grid-based regional groundwater-flow models. SWB makes use of gridded datasets, including datasets describing hydrologic soil groups, moisture-retaining capacity, flow direction, and land use. Climate data may be supplied in gridded or tabular form. The SWB 2.0 code described in this report extends capabilities of the original SWB version 1.0 model by adding new options for representing physical processes and additional data input and output capabilities. New methods included in SWB 2.0 allow for direct gridded input of externally calculated water-budget components (fog, septic, and storm-sewer leakage), simulation of canopy interception by several alternative processes, and a crop-water demand method for estimating irrigation amounts. New input and output capabilities allow for grids with differing spatial extents and projections to be combined without requiring the user to resample and resize the grids before use.

Linking transit times to catchment sensitivity to atmospheric deposition of acidity and nitrogen in mountains of the western United States

Released July 30, 2018 11:55 EST

2018, Hydrological Processes (32) 2456-2470

David W. Clow, M. Alisa Mast, James O. Sickman

Transit times are hypothesized to influence catchment sensitivity to atmospheric deposition of acidity and nitrogen (N) because they help determine the amount of time available for infiltrating precipitation to interact with catchment soil and biota. Transit time metrics, including fraction of young water (Fyw) and mean transit time (MTT), were calculated for 11 headwater catchments in mountains of the western United States based on differences in the amplitude of the seasonal signal of δ18O in streamflow and precipitation. Results were statistically compared with catchment characteristics to elucidate controlling mechanisms. Transit times also were compared with stream solute concentrations to test the hypothesis that transit times are a primary influence on weathering rates and biological assimilation of atmospherically deposited N. Results indicate that transit times in the study catchments are strongly related to soil, vegetation, and topographic characteristics, with barren terrain (bare rock and talus) and steep slopes linked to high Fyw and short MTT, whereas forest soil (hydrogroup B) was linked to low Fyw and greater MTT. Concentrations of silicate weathering products (Na+ and Si) were negatively related to Fyw and barren terrain, and positively related to MTT and forest soil, supporting the concept that weathering fluxes and buffering capacity tend to be low in alpine areas due to short transit times. Nitrate concentrations were positively related to N deposition, catchment slope, and barren terrain, and negatively related to forest, indicating that hydrologic and/or biogeochemical processes associated with steep slopes limit uptake of atmospherically deposited N by biota. Interannual and seasonal variability in transit times and source water contributions in the study catchments was substantial, reflecting the influence of strong temporal variations in snowmelt inputs in high‐elevation catchments of the western United States. Results from this study confirm that short transit times in these areas are a key reason they are highly sensitive to atmospheric pollution and climate change.

Geomorphology and vegetation change at Colorado River campsites, Marble and Grand Canyons, Arizona

Released July 30, 2018 10:19 EST

2018, Scientific Investigations Report 2017-5096

Daniel R. Hadley, Paul E. Grams, Matthew A. Kaplinski, Joseph E. Hazel Jr., Roderic A. Parnell

Sandbars along the Colorado River are used as campsites by river runners and hikers and are an important recreational resource within Grand Canyon National Park, Arizona. Regulation of the flow of river water through Glen Canyon Dam has reduced the amount of sediment available to be deposited as sandbars, has reduced the magnitude and frequency of flooding events, and has increased the magnitude of baseflows. This has caused widespread erosion of sandbars and has allowed native and non-native vegetation to expand on open sand. Previous studies show an overall decline in campsite area despite the use of controlled floods to rebuild sandbars. Monitoring of campsites since 1998 has shown changes in campsite area, but the factors that cause gains and losses in campsite area have not been quantified. These factors include, among others, changes in sandbar volume and slope under different dam flow regimes that include controlled floods, gullying caused by monsoonal rains, vegetation expansion, and reworking of sediment by aeolian processes.

Using 4-band aerial imagery and digital elevation models (DEMs) derived from total-station survey data, we analyzed topographic and vegetation change at 35 of 37 long-term monitoring sites (2 sites were excluded because topographic measurements do not overlap with measurements of campsite area) using data collected between 2002 and 2009 to quantify the factors affecting the size of campsite area. Over the course of the study period, there was a net loss in campsite area of 2,431 square meters (m2). We find that (1) 53 percent of the net loss was caused by topographic change associated with controlled floods and erosion of those flood deposits, (2) 47 percent of the net loss was caused by increases in vegetation cover, the majority of which occurred in high-elevation campsite area, and (3) gullying was significant at certain sites but overall was a minor factor.

Sites in critical reaches—sections of river where campsites are infrequent or where there is high demand by river runners—were subjected to more erosion and changes in sandbar slope than sites in noncritical reaches, suggesting that campsite area is less stable in those reaches. There was also a greater increase in vegetation cover at sites in noncritical reaches than at sites in critical reaches. Our results show a continuation of sandbar erosion and vegetation encroachment that has been occurring at campsites since construction of the dam.

A new campsite survey methodology using a tablet-based geographic information system (GIS) approach was also developed in an effort to map campsite area on digital orthophotographs. Using a series of repeat measurements, we evaluated the inherent uncertainty in mapping campsite area, the accuracy of the new tablet-based method, and if there is any bias between the tablet method and the total-station method that is currently used. We find that uncertainty associated with surveyor judgment while using the total-station method is about 15 percent, which is higher than a previously reported uncertainty of 10 percent. Use of the tablet method adds additional uncertainty; however, the benefits of being able to quantify factors that lead to campsite-area change in the field may outweigh the additional error. Future campsite monitoring may need to consist of a combination of total-station and orthophotograph techniques.

Ghost forests of Marco Island: Mangrove mortality driven by belowground soil structural shifts during tidal hydrologic alteration

Released July 30, 2018 09:31 EST

2018, Estuarine, Coastal and Shelf Science (212) 51-62

Ken W. Krauss, Amanda W.J. Demopoulos, Nicole Cormier, Andrew From, Jennifer McClain Counts, Roy R. Lewis III

Land use changes often create in situ stress and eventual mortality in mangroves as unsuitable hydroperiods are created through tidal flow alterations. Here, we document mangrove forest and soil structural changes within transects established in tidally restricted areas on Marco Island (Collier County, Florida, USA), which has broad swaths of dead-standing or unhealthy mangroves (“ghost forests”). Transects (N = 4) were arranged to include full canopy, transitional, and open canopy (dead) forests, and compared to nearby reference forests. Aboveground and belowground carbon (C) stocks (Total C) ranged from 288 to 304 Mg C ha−1 on full canopy, transitional, and reference sites, which did not differ from each other. However, Total C was lower for dead sites (233 Mg C ha−1) dictated entirely by differences in aboveground C (live and dead trees, downed wood); no differences were found among forest condition in belowground C stocks. This belowground C has been persistent in the soil for 85 years since initial tidal restriction. Nevertheless, hydrologic rehabilitation has the potential to increase total C stocks on dead sites by 70–110 Mg C ha−1. Collapse of the soil surface by 6–8 cm just under the active root zone in chronically stressed mangroves was evident within the bulk density profiles from transitional versus dead sites, suggesting that surface elevation loss as root turnover ceases may work correlatively with chronic stressors (anoxia, P limitation) to affect rapid mortality of forests over short periods of time many years after stress initiation. Hydrologic rehabilitation of stressed or denuded mangroves must also include an understanding of how these soil processes might be re-established.

Vertical zonation and niche breadth of tidal marsh plants along the Northeast Pacific coast

Released July 27, 2018 20:13 EST

2018, Estuaries and Coasts

Christopher N. Janousek, Karen M. Thorne, John Y. Takekawa

The distribution patterns of sessile organisms in coastal intertidal habitats typically exhibit vertical zonation, but little is known about variability in zonation among sites or species at larger spatial scales. Data on such heterogeneity could inform mechanistic understanding of factors affecting species distributions as well as efforts to assess and manage coastal species and habitat vulnerability to sea-level rise. Using data on the vertical distribution of common plant species at 12 tidal marshes across the US Pacific coast, we examined heterogeneity in patterns of zonation to test whether distributions varied by site, species, or latitude. Interspecific zonation was evident at most sites, but the vertical niches of co-occurring common species often overlapped considerably. The median elevation of most species varied across marshes, with site-specific differences in marsh elevation profiles more important than differences in latitude that reflect regional climate gradients. Some common species consistently inhabited lower or higher elevations relative to other species, but others varied among sites. Vertical niche breadth varied more than twofold among species. These results indicate that zonation varies by both site and species at the regional scale, and highlight the potential importance of local marsh elevation profiles to plant vertical distributions. Furthermore, they suggest that coastal foundation species such as marsh plants may differ in their vulnerability to sea-level rise by being restricted to specific elevation zones or by occurring in narrow vertical niches.

Host feeding ecology and trophic position significantly influence isotopic discrimination between a generalist ectoparasite and its hosts: Implications for parasite-host trophic studies

Released July 27, 2018 20:11 EST

2018, Food Webs (16)

William G. Jenkins, Amanda W.J. Demopoulos, Paul C. Sikkel

Despite being one of the most prevalent forms of consumerism in ecological communities, parasitism has largely been excluded from food-web models. Stable isotope analysis of consumers and their diets has been widely used in the study of food webs for decades. However, the amount of information regarding parasite stable isotope ecology is limited, restricting the ability of ecologists to use stable isotope analysis to study parasites in food webs. This study took advantage of distinct differences in the feeding ecology and trophic position of different species of fish known to host the same common micropredatory gnathiid isopod to study the effects of host stable isotope ecology on that of the associated micropredator. Blood engorged juvenile gnathiids were in most cases indistinguishable from their hosts' blood, but significant isotope discrimination was observed for adults. Males were generally lower in δ13C and δ15N than host blood whereas host-specific isotopic discrimination for females varied among the different host species. Model predictions indicated that there is a significant effect of host blood isotope ratios on the rate of carbon and nitrogen isotopic discrimination between gnathiids and their host’s blood. As such, general differences in the feeding ecology and trophic positions of the different host species were reflected in their associated gnathiids, indicating that stable isotope analysis of gnathiids can provide significant details concerning previous hosts. The results presented herein have significant implications for how stable isotopes may be used as a tool to study the trophic dynamics and feeding ecology of gnathiids.

Detections of current-use pesticides at 12 surface water sites in California during a 2-year period beginning in 2015

Released July 27, 2018 13:39 EST

2018, Data Series 1088

Corey J. Sanders, James L. Orlando, Michelle L. Hladik

Surface water samples were collected by the U.S. Geological Survey and multiple cooperators during base flow/irrigation runoff and storm runoff conditions from 12 sites throughout California, over 2 consecutive years beginning in April 2015, from both urban and agriculturally dominated watersheds. Water samples were analyzed by gas chromatography/mass spectrometry and liquid chromatrography/tandem mass spectrometry for a suite of 157 pesticides and degradates. Suspended sediments associated with these water samples were analyzed by gas chromatography/mass spectrometry for a suite of 131 pesticides and degradates. Overall, 85 pesticides and degradates were detected in the water: 32 fungicides, 25 herbicides, 27 insecticides, and 1 synergist. In the suspended sediment, 29 pesticides were detected: 9 fungicides, 10 herbicides, and 10 insecticides. Sixteen pesticides (bifenthrin, carbendazim, chlorpyrifos, clothianidin, diazinon, diuron, fenpyroximate, fipronil, fipronil sulfone, fluopicolide, imidacloprid, metolachlor, novaluron, oxyflurofen, permethrin, and simazine) were detected in the water at concentrations that were above at least one aquatic life benchmark value as defined by the U.S Environmental Protection Agency.

Using reverse-time egg transport analysis for predicting Asian Carp spawning grounds in the Illinois River

Released July 27, 2018 11:13 EST

2018, Ecological Modelling (384) 53-62

Zhenduo Zhu, David T. Soong, Tatiana Garcia, Mina Shahed Behrouz, Steven E. Butler, Elizabeth A. Murphy, Matthew J. Diana, James J. Duncker, David H. Wahl

Identifying spawning grounds of Asian carp is important for determining the reproductive front of invasive populations. Ichthyoplankton monitoring along the Illinois Waterway (IWW) has provided information on abundances of Asian carp eggs in the IWW's navigation pools. Post-fertilization times derived from egg development stages and water temperatures can be used to estimate spawning times of Asian carp eggs, but estimating how far these eggs have drifted requires information on river hydraulics. A Fluvial Egg Drift Simulator (FluEgg) program was designed to predict the drift of Asian carp eggs in the riverine environment with egg growth considered. This paper presents a reverse-time particle tracking (RTPT) algorithm for back-casting the spawning location of eggs from their collection site. The RTPT algorithm was implemented as a module in FluEgg. The new version of FluEgg was coupled with an unsteady hydrodynamic model of the IWW to predict the spawning locations for 530 eggs that were collected in June 2015. The results indicate that tailwater sections below the Locks and Dams (L&Ds) in each navigation pool appear to be preferred spawning locations for Silver Carp. From the data analyzed, the most upstream spawning location for the June 2015 spawning period was in the upper Marseilles navigation pool, downstream of the Dresden Island L&D. The RTPT algorithm can efficiently estimate spawning locations for multiple egg samples.

Rating stability, and frequency and magnitude of shifts, for streamgages in Virginia through water year 2013

Released July 26, 2018 16:45 EST

2018, Scientific Investigations Report 2017-5137

Terence Messinger, Robert W. Burgholzer

The U.S. Geological Survey, in cooperation with the Virginia Department of Environmental Quality, has quantified several measures of rating stability and the frequency and magnitude of changes to ratings through time for 174 real-time continuous streamgages active in Virginia as of September 30, 2013. Generalized additive models (GAMs) were fitted through all available flow measurements for all the streamgages in Virginia’s real-time network as of September 30, 2013, with at least 20 flow measurements with positive flow values. For each measurement with a positive flow value, residuals from the GAM curve were calculated. Time series of these residuals were used to identify major changes to the control (the stream feature or features which control the relation between stage and flow); the measurements in the periods of equilibrium between major changes were assigned to rating families. Of the 127 rating families that were identified as being distinct at sites, documented explanations were found for 67 of them. The most common reasons for the control to change enough to warrant a new rating family are moving the streamgage (28 times), floods (26 times), and construction activities (13 times). Provisional flow data from any streamgage that has recently experienced a major flood, regardless of historical stability, are more uncertain than usual until post-flood evidence emerges that the rating is stable, or if the rating has changed, until it is known to be well defined.

A direct comparison between provisional flow data (those data originally displayed on the web in near-real time) and flow data approved for publication following subsequent flow measurements and review could not be made because provisional flow data have not been archived. As a substitute, alternative flow (AltFlow) tables were constructed for periods with complete records of shifts and ratings. Alternate flows consist of $Q$same, the flow value from the shifted rating table used to compute the daily flow value at the time of the most recent flow measurement that corresponds to the gage height of each day’s daily flow value, and $Q$prev, the flow value from the shifted rating table in effect at the time of the previous flow measurement that corresponds to the gage height of each day’s daily flow value.

Several metrics that summarize AltFlow tables were computed and evaluated; particular importance was given to how well the metrics agreed with the descriptive stability class developed from interviews with hydrographers. Of these stability metrics, at least four were determined to be meaningful and to represent different aspects of control stability that might be relevant to water managers: total root mean square error between log-transformed $Q$prev and $Q$same, percentage of days when the difference between $Q$prev and $Q$same is greater than (>) $Q$same, the sum of absolute AltFlow error divided by total flow, and percentage of days with zero difference between $Q$prev and $Q$same.

Three other meaningful metrics of control stability or provisional flow-data quality were computed: R2 (coefficient of determination) of GAMs from the flow measurements, percentage of total estimated days, and percentage of estimated days in the winter. Correlations among metrics varied, indicating they responded to different aspects of control stability. Relations among the various stability metrics and quantitative basin and site characteristics were weak. Although quantitative relations between stability metrics and basin and site characteristics were all weak, some common patterns still emerged. Controls and ratings on large streams [>500-square mile (mi2) drainage area] and at high elevations (>1,000 feet) were more likely to be stable than controls and ratings on small streams (less than (<) 100-mi2 drainage area) and at low elevations (<500 feet). There were exceptions to both generalizations, and streamgages that were intermediate in both characteristics varied widely in stability.

Typical timing of record computation changed during water years 1991–2013. From 1991 through 2001, the median number of days between the start date of the shift and the date it was created fluctuated between about 240 and about 300 days and decreased by about 4 months from 2001 to 2002. Only in 2012 and 2013 did one-half of the shifts have a delay of about 60 days between start date and final modification.

A method for determining avian influenza virus hemagglutinin and neuraminidase subtype association

Released July 26, 2018 14:15 EST

2018, Open-File Report 2018-1102

Christopher A. Ottinger, Deborah D. Iwanowicz, Luke R. Iwanowicz, Cynthia R. Adams, Lakyn R. Sanders, Christine L. Densmore

Methods for grouping specific avian influenza virus (AIV) hemagglutinin (HA) and neuraminidase (NA) subtype reverse-transcription polymerase chain reaction (RT-PCR) products into HA:NA subtypes when egg incubation is technically not feasible were evaluated. These approaches were adopted for use as post hoc methods after melt curve analysis. The methods are based on ratios obtained from amplicon copy count and amplicon molarity and were founded on the premise that infectious particles contain an equal copy count of single-stranded ribonucleic acid segments that encode HA or NA, and thus subtype-specific amplicons from a single AIV isolate should yield a theoretical HA:NA ratio of 1. Single and mixed HA:NA AIV subtype samples were evaluated to determine whether the calculated HA:NA ratios would approach the theoretical value. With these samples, preference was given to the molarity methods to better define and correct for the effects of multiple potential amplicons in the amplification mix. Further, the molarity method was used to evaluate pond sediment spiked with intact virus of known HA:NA subtype to determine whether the method is sufficiently robust to be used with complex samples, such as those acquired from waterfowl habitat. This was a proof-of-concept study intended to guide future methods development. The methods here are not meant to be applied in any other context.

From the analysis of fully characterized isolates of North American AIV, the HA:NA molarity-based ratios were found to be 1.63 ± 0.75 (mean ± standard deviation) when corrected for the difference in amplification strength and the production of multiple amplicons in some reactions using equations developed in this study. Copy count HA:NA ratios, obtained from HA and NA subtype (RT-qPCR), were 1.146 ± 0.124 (mean ± standard deviation) when corrected for amplification efficiency. Correct associations of HA:NA subtype sample composition were made with mixed samples containing 1 HA and 2 NA, and 2 HA and 2 NA. When spiked pond sediment was evaluated, the molar ratio obtained for the H4 and N6 identified in the sample was 1.28 with correction and 1.14 without correction.

Abundance and productivity of marbled murrelets (Brachyramphus marmoratus) off central California during the 2017 breeding season

Released July 26, 2018 12:39 EST

2018, Data Series 1093

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

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 and evaluation of conservation efficacy, and ultimately to meet Federal- and State-mandated recovery efforts for this species. During June–August 2017, the U.S. Geological Survey Western Ecological Research Center continued previously established, long-term (1999–2016), at-sea surveys to estimate abundance and productivity of marbled murrelets in U.S. Fish and Wildlife Service Conservation Zone 6 (central California—San Francisco Bay to Monterey Bay). Using conventional distance sampling methods, we estimated marbled murrelet abundance using 189 detections of 321 individuals observed on nine unique surveys. The abundance estimated for the entire study area using all surveys in 2017 was 530 birds (95-percent confidence interval, 384–732 birds). Estimated abundance from 2017 is comparable to most prior years of study, except for 2008 and 2015, which had anomalously low abundances. We estimated productivity (calculated as the hatch-year [HY] to after-hatch-year [AHY] ratio) in 2017 using three detections of three individuals observed in 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 0.022 ± 0.014 standard error. We created a synthesized database of all marbled murrelet survey data from 1999 to 2017 to allow scientists and managers to evaluate established survey methods and assess trends in abundance and productivity estimates. Future modifications of survey design could help reduce variance in abundance estimation.

Community for Data Integration 2017 annual report

Released July 26, 2018 12:30 EST

2018, Open-File Report 2018-1110

Leslie Hsu, Madison L. Langseth

The Community for Data Integration (CDI) is a group that helps members grow their expertise on all aspects of working with scientific data. The CDI’s activities advance data and information integration capabilities in the U.S. Geological Survey and in the wider Earth and biological sciences. This annual report describes the presentations, activities, collaboration areas, workshop, and other CDI-sponsored events in fiscal year 2017. The report also describes the objectives of the 11 CDI-funded projects in fiscal year 2017. The report shows how the CDI activities fulfill the strategic objective of the U.S. Geological Survey’s Core Science Systems Mission Area to develop a workplace model for interdisciplinary science.

Spatial and temporal trends in selenium in the upper Blackfoot River watershed, southeastern Idaho, 2001–16

Released July 26, 2018 11:59 EST

2018, Scientific Investigations Report 2018-5081

Lauren M. Zinsser, Christopher A. Mebane, Greg C. Mladenka, Lynn R. Van Every, Marshall L. Williams

Phosphate mining in southeastern Idaho has been an important economic driver for the region and State for over 100 years, but weathering of mining waste rock has also released selenium into the Blackfoot River. This report analyzes and presents data from three separate but complementary studies monitoring selenium in streams in the region. The U.S. Geological Survey (USGS), in cooperation with the Bureau of Land Management, has been collecting streamflow and water-quality samples year-round on the Blackfoot River above reservoir near Henry, Idaho, (USGS streamgage 13063000) since 2001. Over the same period, the Idaho Department of Environmental Quality (IDEQ) has collected streamflow and water-quality samples from the Blackfoot River and tributaries during spring runoff. Data collected from 2001 to 2012 during these two studies were analyzed previously. This report extends the analysis using new data collected through 2016. This report also presents the results of a joint USGS and IDEQ seepage study conducted in June 2016 in the Blackfoot River near Dry Valley. Although limited in scope, this study explored the hypothesis that unaccounted selenium loading (loading in excess of tributary inputs) in this reach could be caused by groundwater inflow.

USGS dissolved selenium concentration data from streamgage 13063000 on the Blackfoot River and IDEQ data from the mainstem and mining-affected tributaries are highest shortly after peak runoff and correlate with streamflow magnitude. Although earlier analyses indicated increasing selenium concentrations from 2001 to 2012, this study shows that runoff and baseflow dissolved selenium concentrations increased and then decreased during 2001–16. High median runoff concentrations from 2005 through 2011 are associated with high snowpack and streamflow. This result suggests that more snowmelt moving through selenium-bearing waste rock leads to increased instream concentrations. The time lag between peak runoff and then peak selenium concentrations suggests that selenium mobilization may occur as snowmelt percolates through waste rock rather than by faster surface runoff. However, variability in local snow accumulation and snowmelt conditions likely affects interannual variability in selenium concentrations in the mainstem Blackfoot River and tributaries.

In contrast to runoff selenium concentrations, median baseflow (August to October) dissolved selenium concentrations were highest from 2009 to 2013. Aquatic plant senescence and release of selenium is an unlikely explanation for this trend because plants are still growing during this time of year. In addition, this trend is observed during and shortly after the observed period of high snowpack. Thus, increased baseflow selenium concentrations suggest that increased selenium loading to alluvial groundwater may occur during periods of high snowmelt and manifest in later years as higher instream concentrations during baseflows when the majority of streamflow is attributable to groundwater gains.

Runoff-period streamflow and selenium loads were calculated for the tributaries and mainstem Blackfoot River. Selenium loads vary from year to year with mainstem loads greater than the total tributary contributions in some years and less than tributary contributions in other years. In general, East Mill Creek usually accounted for the largest proportion of the total Blackfoot River load, and unaccounted loads (loads in excess of tributary inputs) often occurred in the vicinity of Spring Creek and Dry Valley. The latter observation led the USGS and IDEQ to conduct a seepage study to further investigate groundwater and selenium loading to the Blackfoot River near Dry Valley.

The seepage study results show consistent albeit small unaccounted increases in streamflow and dissolved selenium load in the Blackfoot River near Dry Valley. Field observation of a spring to the north of the river and independent groundwater monitoring data from Dry Valley to the south of the river suggest that alluvial groundwater may discharge to the river from both sides. However, the small unaccounted selenium load measured in the June 2016 study relative to loads measured during runoff suggest that groundwater loading in this reach may occur primarily during runoff. An improved understanding of alluvial groundwater extent, gradient, hydraulic conductivity, and quality would aid in interpreting unaccounted gains and losses in selenium loads in the Blackfoot River.

Finally, State of Idaho selenium water-quality criteria have recently shifted to a hierarchical fish tissue and water concentration scheme. This report summarizes existing fish tissue and water-quality data in the mainstem and offers considerations for future selenium monitoring in the Blackfoot River.

UFINCH: A method for simulating unit and daily flows in networks of channels described by NHDPlus using continuous flow data at U.S. Geological Survey streamgages

Released July 26, 2018 11:30 EST

2018, Scientific Investigations Report 2016-5074

David J. Holtschlag

The UFINCH (Unit Flows In Networks of Channels) computer application can be used to simulate daily and unit flows in networks of streams based on geospatial data in the National Hydrography Dataset NHDPlus (with value added attributes), and U.S. Geoogical Survey daily streamflow data from a downstream (or base) streamgage. Among streamflow augmentation methods, UFINCH has the unique capability to estimate time series of flows from a single base (downstream) streamgage to many upstream reaches, while conserving flows within the basin. UFINCH also provides a simple statistical model to adjust simulated flows to better match continuous flows from data at an upstream streamgage. Parameters of the statistical model are estimated using overlapping periods of record at the two streamgages, but the adjustment can be applied to all years of record available at the base streamgage. This report describes the main features of UFINCH and presents results from a sample application. Interactive graphical user interfaces and automated geographical information processing facilitate flow-data retrievals provide an intuitive environment for efficient and effective generation of flow information in a network. UFINCH is coded in the Matlab programming language and can be run in the Matlab programming environment, with supporting statistical, optimization, and mapping toolboxes, or from compiled code on a Microsoft Windows computer.

Comparison of regression relations of bankfull discharge and channel geometry for the glaciated and nonglaciated settings of Pennsylvania and southern New York

Released July 25, 2018 16:00 EST

2018, Scientific Investigations Report 2018-5066

John W. Clune, Jeffrey J. Chaplin, Kirk E. White

Streambank erosion in areas of past glacial deposition has been shown to be a dominant source of sediment to streams. Water resource managers are faced with the challenge of developing long and short term (emergency) stream restoration efforts that rely on the most suitable channel geometry for project design. A geomorphic dataset of new (2016, n=5) and previous (1999–2006, n=96) estimates of bankfull discharge and channel dimensions at U.S. Geological Survey streamflow-gaging stations was compiled to present and contrast the glaciated and unglaciated noncarbonate settings of southern New York and Pennsylvania that included selected areas of Maryland. Empirical models were developed by using simple linear regressions that relate bankfull discharge and channel geometry to drainage area (regional curves). Significant relations (p<0.05) were able to explain variability with coefficient of determination (R2 ) values of 0.89 for bankfull discharge, 0.94 for cross-sectional area, 0.87 for bankfull width, and 0.83 for bankfull depth. These regression relations for the glaciated noncarbonate settings of northern Pennsylvania and southern New York were able to provide a slightly better fit than regional curve models developed previously for the entire noncarbonate region of Pennsylvania. Although, the analysis of covariance (ANCOVA) results for comparison between regression equations for the glaciated and unglaciated settings showed that except for the significant intercept of bankfull discharge versus drainage area (F=8.26, p-value<0.005), the regression equations are not significantly different between the glaciated and unglaciated setting of Pennsylvania and southern New York. Therefore, data stratification by glaciation does not improve regional curves relations developed previously for the noncarbonate (glaciated and unglaciated) and carbonate settings of Pennsylvania and Maryland. Further analysis that incorporates data stratification or multivariate approaches based on mean annual runoff, precipitation, slope, stream classification, or other relevant parameters may optimize the accuracy and utility of statewide models. The new estimates of bankfull discharge and channel dimensions at streamflowgaging sites and updated drainage areas from StreamStats were incorporated into previously developed regional curves to produce an updated set of regression relations of bankfull discharge and channel geometry for the noncarbonate and carbonate settings of Pennsylvania and Maryland.

Geochemistry and microbiology of groundwater and solids from extraction and monitoring wells and their relation to well efficiency at a Federally operated confined disposal facility, East Chicago, Indiana

Released July 24, 2018 11:00 EST

2018, Scientific Investigations Report 2018-5073

E. Randall Bayless, Travis R. Cole, David C. Lampe, Rebecca E. Travis, Marjorie S. Schulz, Paul M. Buszka

In cooperation with the U.S. Army Corps of Engineers, Chicago District, the U.S. Geological Survey investigated the processes affecting water quality, geochemistry, and microbiology in representative extraction and monitoring wells at a confined disposal facility (CDF) in East Chicago, Indiana. The CDF is a 140-acre Federally-managed facility that was the former location of an oil refinery and is now used for the long-term disposal and storage of dredge material from the Indiana Harbor and Indiana Harbor Canal. Residual petroleum hydrocarbons and leachate from the CDF are contained within the facility by use of a groundwater cutoff wall. The wall consists of a soil-bentonite slurry and a gradient control system made up of an automated network of 96 extraction wells, 42 monitoring wells, and 2 ultrasonic sensors that maintain an inward hydraulic gradient at the site. The pumps in the extraction wells require vigilant maintenance and must be replaced when unable to withdraw water at a rate sufficient to maintain the required inward gradient. The wells are screened in the Calumet aquifer, a coarse-grained sand and gravel unit that extends approximately 35 feet below the land surface and is not utilized for drinking-water supply at the CDF or in the surrounding area. This study was initiated to identify the cause of decreased pump discharges and to identify potential mitigation strategies.

For this study, the U.S. Geological Survey collected groundwater and solids from monitoring and extraction wells. Groundwater samples were collected during June 2014 for precautionary health screening and on four occasions during September 2014 through November 2014. Groundwater samples collected from two extraction wells during June 2014 were analyzed for concentrations of anthropogenic organic constituents. During September through November 2014, groundwater samples were collected from one additional extraction well, and samples from three monitoring wells were analyzed for concentrations of inorganic and organic constituents, dissolved gases, and bacterial abundance and diversity. Solid samples were collected during April 2014, during September 2014 through November 2014, and during November 2016. Solid samples were collected from the exterior of extraction-well pumps and as flocculent from water samples. Solid samples were collected from 10 wells, including 1 extraction well and 3 monitoring wells sampled for water quality. Solid samples were analyzed for mineralogy, solid-phase habit, geochemistry, and organic composition.

The following is a list of observations that were made during this study: (1) the water quality is substantially variable among the six well locations sampled as part of this study—lower (more negative) redox values and higher concentrations of many constituents (including calcium, magnesium, sodium, and sulfate) and properties (including dissolved solids, hardness, and turbidity) were detected in sampled wells located near the extraction wells with the highest frequency of failure; (2) water-level drawdown is variable between extraction wells—wells with the greatest drawdown may pull deeper groundwater into the borehole; (3) dissolved gas results indicate reducing oxidation-reduction processes in the aquifer material that can feasibly contribute iron, carbon dioxide, and other byproducts from hydrocarbon degradation to precipitates and solids that accumulate on and impair pump operation; (4) crystalline and amorphous solid-phase minerals are precipitating in the borehole; (5) several types of bacteria are present in water pumped from extraction wells and are likely responsible for bonding mineral and microbiologic matter to the pump (and other well components); and (6) bacteria may create microenvironments that facilitate precipitation of solids or inhibit dissolution of unstable minerals once the bacteria adhere to biofilm attached to the pump. Results of the study indicate that bacteria may be accumulating and entrapping solid material on the exterior of pumps. This accumulation reduces heat transfer and water discharge from the pump and may lead to decreased efficiency or mechanical failure. Observations could not be made on the well screen, gravel pack, or surrounding geologic formation; therefore, mitigating measures in the borehole may not solve well-productivity issues.

Remedies for the pump fouling problems were derived from the review and interpretation of data collected during this study and from information documented in other sources about groundwater well fouling. Potential remedies to problems associated with pump fouling at the CDF may include the following: (1) reducing attractiveness of the extraction wells for microbiological growth by modifying the chemical or physical environment of the well, (2) modifying the pump exterior to decrease microbiological adherence, (3) changing the pumping regime to control the chemistry of water entering the well from the surrounding aquifer material, (4) modifying the pumps to be less physically and thermally attractive, and (5) removing hydrocarbons from groundwater and the aquifer material surrounding the wells or adding surfactants to make them more mobile. Pilot scale testing may be necessary to identify the most effective treatment or combination of treatments.

Groundwater discharge characteristics for selected streams within the Loup River Basin, Nebraska, 2014–16

Released July 24, 2018 00:00 EST

2018, Scientific Investigations Report 2018-5093

Christopher M. Hobza, Aaron R. Schepers

Streams in the Loup River Basin are sensitive to groundwater withdrawals because of the close hydrologic connection between groundwater and surface water. Groundwater discharge is the primary component of streamflow in the Loup River Basin and constitutes more than 90 percent of streamflow in the central part of the Sand Hills. To improve the understanding of geologic controls and various climatic and land-use changes on groundwater discharge, the U.S. Geological Survey (USGS), in cooperation with the Upper Loup Natural Resources District (NRD), the Lower Loup NRD, and the Nebraska Environmental Trust, studied the spatial and temporal characteristics of groundwater discharge within the Loup River Basin. This report documents the methods of data collection and analysis, which include the collection of approximately 350 river miles of aerial thermal infrared imagery and continuous groundwater-level and temperature data from six streamflow-gaging stations within the Loup River Basin.

The results from the stream reconnaissance and examination of aerial thermal infrared imagery demonstrated the influence of the surficial and subsurface geology on the spatial characteristics of groundwater discharge to streams in the Loup River Basin. At the headwaters of the South Loup River, streamflow is sustained and increased from focused groundwater discharge emanating from Quaternary deposits at many small (less than 0.1 cubic foot per second) focused points. The volume of water produced from this dense network of focused groundwater discharge points along the North Fork South Loup River is sufficient to provide approximately 40 percent of the flow measured at the South Loup River at Arnold, Nebraska streamflow-gaging station (USGS station 06781600) during the irrigation season. Approximately 5 miles downstream from the South Loup River at Arnold, Nebr., streamflow-gaging station, the river incises into Pliocene-age sand and gravel deposits, which provide additional groundwater discharge to the stream. The streamflow of the South Loup River increases by a factor of 5 across a 62-mile reach of the middle South Loup River.

Increases in streamflow along the upper Dismal River result from a dense network of focused groundwater discharge points within semiconsolidated Pliocene-age deposits. Below the Dismal River near Thedford, Nebr., streamflow-gaging station (USGS station 06775900), the Dismal River incises into the Ogallala Formation over a short reach before flowing over coarser, more permeable Quaternary-age alluvial deposits. Diffuse groundwater discharge sustains and increases the streamflow of the lower Dismal River in this reach.

Groundwater sapping was evident on some stream reaches and has increased the size and flow of focused groundwater discharge points. Previous researchers have documented streambed incision and groundwater sapping on the upper Dismal River that have created and enlarged focused groundwater discharge points capturing additional groundwater. Similar processes appear to have played a role in the formation of larger focused groundwater discharge points, which sustain the flow of the middle South Loup River. The constant flow of groundwater into the South Loup River has removed finer-grained Quaternary sediments and further exposed Pliocene-age gravel deposits. Headward erosion is evident where some of the large focused groundwater discharge points have incised their own draws and terminate in bowl-like depressions away from the stream.

Within the Loup River NRDs, the percentage of groundwater-irrigated land in a stream basin is one factor that affects groundwater discharge to streams. A striking example was at the South Loup River at Saint Michael, Nebr., groundwater and streamflow-gaging station (USGS station 06784000) where the shallow groundwater levels declined below the level of the stream during the middle to late part of the growing season (July to September) when consumptive groundwater use was at its peak. The South Loup River Basin above the South Loup River at Saint Michael, Nebr., streamflow-gaging station has the highest percentage of groundwater-irrigated row crops of all the basins examined in this study. Continuous groundwater and surface-water levels measured at the North Loup River at the Taylor, Nebr., streamflow-gaging station (USGS station 06786000) indicate that the stream is receiving groundwater throughout the year; however, when consumptive groundwater use peaks during the middle to late part of the growing season (July to September), the difference in elevation between the groundwater level and the stream elevation decreases, which indicates a reduction in the amount of groundwater discharge received.

Preliminary groundwater salinity mapping near selected oil fields using historical water-sample data, central and southern California

Released July 24, 2018 00:00 EST

2018, Scientific Investigations Report 2018-5082

Loren F. Metzger, Matthew K. Landon

The distribution of groundwater salinity was mapped for 31 oil fields and adjacent aquifers and summarized by 8 subregions across major oil-producing areas of central and southern California. The objectives of this study were to describe the distribution of groundwater near oil fields having total dissolved solids less than 10,000 milligrams per liter (mg/L) based on available data and to document where data gaps exist. Salinity was represented by the measured or calculated concentration of total dissolved solids (TDS) in samples of produced water obtained from petroleum wells and groundwater obtained from water wells. The water chemistry data were used to estimate the minimum depths of TDS greater than 3,000 mg/L and greater than 10,000 mg/L in areas near selected oil fields using historical water-chemistry data coupled with available well-location and construction information.

The 10,000 mg/L threshold, representing the highest level of TDS concentration of water that could be considered as a potential source of drinking water, was present in all but 4 (Jasmin, Kern Bluff, Kern Front, and Mount Poso) of the 31 individual oil fields. Among petroleum wells, the median TDS concentration of produced water ranged from 500 mg/L for the Jasmin field to 32,636 mg/L for the Elk Hills field. Among water wells, median TDS concentrations, either reported or calculated from specific conductance, ranged from 151 mg/L for wells within 2 miles of the Ten Section field to 9,750 mg/L for wells within 2 miles of the combined North and South Belridge fields.

In general, TDS across the eight geographic subregions increased with depth, but the relation of TDS with depth varied regionally. The most pronounced increases in TDS with depth were across the West Kern Valley Floor and West Kern Valley Margin subregions on the west side of the San Joaquin Valley, and in the vicinity of the Wilmington field in the Los Angeles Basin subregion; in these areas, relatively high TDS concentrations greater than 10,000 mg/L were present within the upper few hundred to several thousand feet of land surface. Total dissolved solids concentrations increased more gradually with depth in the Middle Kern Valley Floor subregion, in the South Kern Valley Margin subregion, in the vicinity of the Montebello and Santa Fe Springs fields in the Los Angeles Basin subregion, and in the Central Coast Basin subregion. The Kern Sierran Foothills and East Kern Valley Floor subregions, on the east side of the San Joaquin Valley, had the most gradual increases in TDS with depth. Fields in the East Kern Valley Floor subregion generally had groundwater and produced water with TDS less than 10,000 mg/L that extended to a large depth compared to most other subregions.

Overall, the west side of the San Joaquin Valley in Kern County and the Wilmington field in Los Angeles County generally have the highest TDS values and the shallowest depths to high TDS. High TDS at relatively shallow depths on the west side of the San Joaquin Valley may be because of a combination of natural conditions and anthropogenic factors. In the vicinity of the Wilmington field in the Los Angeles Basin subregion, high TDS at relatively shallow depths is attributable at least in part to seawater intrusion. Fields on the east side of the San Joaquin Valley in Kern County have the lowest TDS and greatest depths to TDS greater than 10,000 mg/L because of their geologic setting adjacent to Sierra Nevada recharge areas.

Reconnaissance salinity mapping was limited by several factors. The primary limitation was the lack of well-construction data for a significant number of water wells. Bottom perforation, well depth, or hole depth were not available for 35 percent of wells used for salinity mapping. A second limitation was variability in data quality. Total dissolved solids and specific conductance data were compiled from different data sources with varying degrees of documentation that ranged from comprehensive to very little or none. As a result, it was not always possible to assess the quality of the provided data with respect to either conditions at each well during sampling or the methodology used for sample collection and analysis. A third limitation was the lack of wells, either petroleum or water, and associated TDS data over large vertical intervals for some fields. As a result, the distribution of salinity and the depths at which TDS concentration exceeds the 3,000 and 10,000 mg/L thresholds could not always be precisely determined. This analysis highlights key gaps that need to be filled with additional analysis of other sources of information, such as borehole geophysical logs and new water sample or geophysical data collection.

Survival, travel time, and utilization of Yolo Bypass, California, by outmigrating acoustic-tagged late-fall Chinook salmon

Released July 23, 2018 00:00 EST

2018, Open-File Report 2018-1118

Adam C. Pope, Russell W. Perry, Dalton J. Hance, Hal C. Hansel

Juvenile Chinook salmon (Oncorhynchus tshawytscha) migrating through California's Sacramento-San Joaquin River Delta toward the Pacific Ocean face numerous challenges to their survival. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 70 percent of years in response to large, uncontrolled runoff events. As one of the routes juvenile salmon may utilize, the Yolo Bypass has recently received attention for having potential benefit to rearing and migrating salmon. Consideration is being given to a plan to build a cut or “notch” in the Fremont Weir to increase juvenile salmon access to the Yolo Bypass. To help provide information about the potential benefit of such a plan, we analyzed data from a telemetry study conducted in February and March 2016 by the U.S. Geological Survey and California Department of Water Resources to estimate entrainment into and distribution of juvenile Chinook salmon within the Yolo Bypass, and to compare survival and travel time through the Yolo Bypass to other routes in the Delta. We also estimated juvenile Chinook salmon survival through three short reaches of the Sacramento River where the proposed California WaterFix North Delta Diversion intakes would divert water to export facilities to provide baseline information against which any effects of those intakes could be measured in the future.

We found that entrainment into the Yolo Bypass varied widely and was quite high only at the peak of the March 2016 flood. Spatial distribution of juvenile Chinook salmon within the Yolo Bypass was fairly even for fish entering the Yolo Bypass over the Fremont Weir, but increasingly skewed toward the east bank for fish released within the Yolo Bypass. Survival within Yolo Bypass was not significantly different for fish based on spatial distribution. Survival through the Delta for fish migrating through the Yolo Bypass was generally on par with the weighted survival through the Delta of fish migrating through all other routes. Survival was highest for fish remaining in the Sacramento River and lowest for those entrained into the Interior Delta via Georgiana Slough. Survival through the short section of the Sacramento River near the proposed North Delta Diversion intakes was high.

Evaluation of sockeye salmon after passage through an innovative upstream fish-passage system at Cle Elum Dam, Washington, 2017

Released July 23, 2018 00:00 EST

2018, Open-File Report 2018-1116

Tobias J. Kock, Scott D. Evans, Amy C. Hansen, Russell W. Perry, Hal C. Hansel, Philip V. Haner, Ryan G. Tomka

Executive Summary

The Bureau of Reclamation (Reclamation) and the Washington State Department of Ecology (Ecology), working with the Yakima River Basin Water Enhancement Project Workgroup (composed of representatives of the Yakama Nation; Federal, State, county, and city governments; environmental organizations; and irrigation districts), developed the Yakima Basin Integrated Plan (Integrated Plan). The Integrated Plan identifies a comprehensive approach to water resources and ecosystem restoration improvements in the Yakima Basin to be implemented over a 30-year period. The Integrated Plan includes seven elements:

  1. Reservoir fish passage,
  2. Structural and operational changes to existing facilities,
  3. Surface water storage,
  4. Groundwater storage,
  5. Habitat/watershed protection and enhancement,
  6. Enhanced water conservation, and
  7. Market reallocation.

The first listed element, reservoir fish passage, will be expensive and take many years to accomplish. Reclamation and Ecology decided to look at new and innovative means to provide passage that could help reduce project cost and construction timing while maintaining survival rates of traditional upstream passage facilities. Reclamation contracted with the U.S. Geological Survey to do a study to evaluate the outcome of passage through one innovative fish-passage system at Cle Elum Dam, the first Integrated Plan reservoir fish-passage project being implemented.

Monitoring breeding and migration of neotropical migratory birds at Naval Base Coronado, Remote Training Site, Warner Springs, San Diego County, California, 5-year summary, 2013–17

Released July 23, 2018 00:00 EST

2018, Open-File Report 2018-1112

Suellen Lynn, Katie A. Hall, Melanie C. Madden, Barbara E. Kus

We operated a bird banding station on the Naval Base Coronado, Remote Training Site, Warner Springs (RTSWS), in northeastern San Diego County, California, during the bird breeding season (spring/summer) from 2013 to 2017 and during migration (fall) from 2013 to 2016. The station was established in spring 2013 as part of the Monitoring Avian Productivity and Survivorship (MAPS) program and continued into the fall for the first 4 years as part of a long-term monitoring program for neotropical migratory birds.

We captured 705 individuals of 58 species during the MAPS/breeding season from 2013 to 2017 (12–13 days each year in April through August), 79 percent of which were newly banded during the MAPS season (555), 8 percent of which were recaptures banded in previous years (57), and 13 percent of which we released unbanded (64 hummingbirds and 29 other birds that were released or escaped prior to banding). Sixty individuals were captured more than once within a year during MAPS. Bird capture rate averaged 19 ± 1 captures per 100 net-hours (range 17–20) across 5 years. Annual species richness ranged from 28 (2017) to 42 (2014). The average species richness per day was highest in 2014 (9 ± 3) and lowest in 2016 (6 ± 2). Bushtit (Psaltriparus minimus) was the most abundant breeding species captured, followed by Spotted Towhee (Pipilo maculatus), Oak Titmouse (Baeolophus inornatus), Anna’s Hummingbird (Calypte anna), House Wren (Troglodytes aedon), Ash-throated Flycatcher (Myiarchus cinerascens), California Scrub-jay (Aphelocoma californica), Bewick’s Wren (Thryomanes bewickii), Acorn Woodpecker (Melanerpes formicivorus), California Towhee (Melozone crissalis), and Western Bluebird (Sialia mexicana). Each of these 11 breeding species accounted for at least 5 percent of captures in any 1 year. Fifty-seven percent of known-sex captures were female and 43 percent were male. Thirty-three percent of known-age captures were juveniles. Peaks in number of birds captured were in the first and last weeks of April, and the greatest number of species was captured in early May.

Refinement of a regression-based method for prediction of flow-duration curves of daily streamflow in the conterminous United States

Released July 23, 2018 00:00 EST

2018, Scientific Investigations Report 2018-5072

Thomas M. Over, William H. Farmer, Amy M. Russell

Regional regression is a common tool used to estimate daily flow-duration curves (FDCs) at ungaged locations. In this report, several refinements to a particular implementation of the regional regression method for estimating FDCs are evaluated by consideration of different methodological options through a leave-one-out cross-validation procedure in the 19 major river basins of the conterminous United States. Regression analyses in this report are based on streamflow data from water years 1981–2013 (October 1, 1980 to September 30, 2013) from 1,378 mostly undisturbed watersheds. Linear regression using selected basin characteristics at 27 quantiles with nonexceedance probabilities ranging from 0.02 to 99.98 percent was applied. The regression computations were primarily by weighted least squares, with left-censored Gaussian regression solved by maximum likelihood in the presence of zero-valued quantiles.

The regional regression method as applied to the FDC estimation problem includes several methodological options that require determination of the better of two or more choices. The options considered in this report include (1) the setting of the maximum number of basin characteristics considered in the regression models for each region, (2) the method of placing the quantiles into groups (“flow regimes”) having the same basin characteristics used as independent variables, (3) the maximum number of candidate models retained from regressions at the single-quantile level that are retained for testing of the best model at the flow-regime scale, and (4) whether drainage area should be forced into the models. In all, 5 binary options were considered for most regions, resulting in 32 methodological combinations. Leave-one-out cross-validation predictions of FDC quantiles at each streamgage used in the study were used to evaluate compared options. Various performance measures were computed based on the predicted quantiles; these were combined by region and the methods were ranked for each measure.

Based on examination of the ranked methods compared across the measures, the following treatments produced the more accurate results: (1) using fewer basin characteristics (of the two options considered), (2) utilizing a variance of the unit FDC-based method of determining the flow regimes rather than fixed regimes, (3) retaining more models from the quantile-level regressions regime-wide consideration, and (4) forcing drainage area into the regression models. Results of analyses also indicate that performance varies more by region than by methodological option, with FDCs in arid regions and those with a large value of a measure of intraregional FDC heterogeneity being harder to predict, particularly with respect to the low-flow quantiles.

U.S. Geological Survey response to white-nose syndrome in bats

Released July 20, 2018 15:15 EST

2018, Fact Sheet 2018-3020

M. Camille Hopkins, Suzanna C. Soileau


Since its discovery in 2007, the fungal disease known as white-nose syndrome (WNS) has killed more than six million bats. Ten of 47 bat species have been affected by WNS across 32 States and 5 Canadian Provinces. The cold-growing fungus (Pseudogymnoascus destructans) that causes WNS infects skin covering the muzzle, ears, and wings of hibernating bats. The fungus erodes deep into the vitally important skin of bat wings and fatally disrupts hibernation of bats through physical damage and energy depletion as they try to cope with infection.

U.S. Geological Survey (USGS) science has been critical in identifying the causal fungus, characterizing the effects of WNS, and tracking the fungus as it rapidly spreads through many populations of bats in North America. Early USGS research enhanced our understanding of how WNS affects individual bats and how the fungus persists in the environment. Today, USGS scientists are engaged in a nationwide response to WNS, in close coordination with our partners at the U.S. Fish and Wildlife Service (USFWS), National Park Service (NPS), and U.S. Forest Service (USFS).

The influence of different deep-sea coral habitats on sediment macrofaunal community structure and function

Released July 20, 2018 14:35 EST

2018, PeerJ (6) 1-32

Jill R. Bourque, Amanda W.J. Demopoulos

Deep-sea corals can create a highly complex, three-dimensional structure that facilitates sediment accumulation and influences adjacent sediment environments through altered hydrodynamic regimes. Infaunal communities adjacent to different coral types, including reef-building scleractinian corals and individual colonies of octocorals, are known to exhibit higher macrofaunal densities and distinct community structure when compared to non-coral soft-sediment communities. However, the coral types have different morphologies, which may modify the adjacent sediment communities in discrete ways. Here we address: (1) how infaunal communities and their associated sediment geochemistry compare among deep-sea coral types (Lophelia pertusa, Madrepora oculata, and octocorals) and (2) do infaunal communities adjacent to coral habitats exhibit typical regional and depth-related patterns observed in the Gulf of Mexico (GOM). Sediment push cores were collected to assess diversity, composition, numerical abundance, and functional traits of macrofauna (>300 µm) across 450 kilometers in the GOM at depths ranging from 263–1,095 m. Macrofaunal density was highest in L. pertusa habitats, but similar between M. oculata and octocorals habitats. Density overall exhibited a unimodal relationship with depth, with maximum densities between 600 and 800 m. Diversity and evenness were highest in octocoral habitats; however, there was no relationship between diversity and depth. Infaunal assemblages and functional traits differed among coral habitats, with L. pertusa habitats the most distinct from both M. oculata and octocorals. These patterns could relate to differences in sediment geochemistry as L. pertusa habitats contained high organic carbon content but low proportions of mud compared to both M. oculata and octocoral habitats. Distance-based linear modeling revealed depth, mud content, and organic carbon as the primary factors in driving coral infaunal community structure, while geographic location (longitude) was the primary factor in functional trait composition, highlighting both the location and ecological differences of L. pertusa habitats from other coral habitats. Enhanced habitat structural complexity associated with L. pertusa and differences in localized hydrodynamic flow may contribute to the dissimilarities in the communities found among the coral types. Our results suggest a decoupling for infaunal coral communities from the typical depth-related density and diversity patterns present throughout soft-sediment habitats in the GOM, highlighting the importance of deep-sea corals in structuring unique communities in the nearby benthos.

Findings from a preliminary investigation of the effects of aquatic habitat (water) availability on giant gartersnake (Thamnophis gigas) demography in the Sacramento Valley, California, 2014–17

Released July 20, 2018 00:00 EST

2018, Open-File Report 2018-1114

Jonathan P. Rose, Julia S. M. Ersan, Gabriel A. Reyes, K. Benjamin Gustafson, Alexandria M. Fulton, Kristen J. Fouts, Raymund F. Wack, Glenn D. Wylie, Michael L. Casazza, Brian J. Halstead

The giant gartersnake (Thamnophis gigas) is a semi-aquatic species of snake precinctive to the Central Valley of California. Because the Central Valley has experienced a substantial loss of wetland habitat, giant gartersnake populations are largely found in aquatic habitats associated with rice agriculture. In dry years, less water may be available for rice agriculture, resulting in less aquatic habitat, which could have cascading effects on giant gartersnake populations. We present 2 years of data intended to examine how the demography of giant gartersnakes is affected by the availability of aquatic habitat on the landscape (2016–17), along with 2 years of (sparse) preliminary data (2014–15) collected as part of an earlier radio-telemetry study on giant gartersnake movement behavior. We sampled agricultural canals near rice fields for giant gartersnakes at 8 sites distributed throughout the Sacramento Valley. Five sites were sampled from 2014–17, and 3 sites were sampled from 2015–17. In total, we made 2,995 captures of 1,011 snakes from 2014–17. We used these capture data to fit a multi-site Jolly-Seber model to estimate the abundance of giant gartersnakes as well as the daily and annual probability of capture at each site. We used remotely sensed Landsat data to characterize the extent of flooded rice fields surrounding each site in each year. In addition, we collected 175 females from 2014–17 and delivered them to the Sacramento Zoo for health assessments and reproductive exams.

The abundance of giant gartersnakes varied among sites, and abundance estimates were more precise in 2016 and 2017 when sampling effort was greatest. The probability of a giant gartersnake being captured at least once in a year was higher in 2016 and 2017 than 2014 and 2015, and recaptures of snakes marked the previous year were highest in 2016 and 2017 as well. Mean annual apparent survival was estimated to be 0.40 but varied among sites from a low of 0.14 to a high of 0.63. Five sites had diverse size distributions that included abundant sub-adult and large adult female snakes. One site had a truncated size distribution with few large adult female snakes, and 2 sites had mostly large adult-sized snakes and few small individuals. Both the probability a female was gravid and a female’s litter size were positively related to the female’s snout-vent length. Somatic growth rates varied more among years than among sites, and females grew faster (in millimeters per day) than male snakes.

The proportion of the landscape around each site under active rice cultivation fluctuated over time (generally between 60–90 percent of the landscape was active rice growing, although this proportion was lower for some sites in some years), and variation in rice growing was asynchronous among sites. This study demonstrates that intensive demographic sampling enables estimation of several key demographic variables at each study site. Continued sampling would allow for investigating potential relationships between the amount of rice growing at a site and demographic parameters such as growth, survival, and reproduction.

Coeur d’Alene Basin Environmental Monitoring Program, surface water, northern Idaho—Annual data summary, water year 2017

Released July 20, 2018 00:00 EST

2018, Open-File Report 2018-1113

Lauren M. Zinsser

Streams within the Coeur d’Alene River drainage basin in northern Idaho have been extensively affected by historical mining activities and are subject to ongoing remedial actions as part of the Bunker Hill Mining & Metallurgical Complex Superfund Site. The U.S. Geological Survey (USGS) operates 12 real-time streamgages and collects surface-water-quality samples two to four times annually at 20 sites in the Spokane River and Coeur d’Alene River drainage basins. These data are used by the U.S. Environmental Protection Agency (USEPA) to monitor cleanup progress and to support decisions related to implementing remedial actions throughout the basin. USGS data collection highlights from water year 2017 include: • A rain-on-snow event in March 2017 produced high streamflows and flooding in the basin. • The March event mobilized high concentrations of total metals (cadmium, lead, zinc, and others) in the Coeur d’Alene River near Cataldo, at Rose Lake, and near Harrison; these concentrations were among the highest that have been measured at these sites during flood events sampled by the USGS. • Total lead and dissolved zinc and cadmium concentrations decreased in Canyon Creek in 2017 when compared with water years 2007–16; in contrast, concentrations of dissolved zi

Quality-assurance plan for groundwater activities, U.S. Geological Survey Dakota Water Science Center

Released July 20, 2018 00:00 EST

2018, Open-File Report 2018-1103

Joshua F. Valder, Janet M. Carter, Steven M. Robinson, Christopher D. Laveau, Joel A. Petersen

As the Nation’s principal earth-science information agency, the U.S. Geological Survey (USGS) is depended upon to collect accurate data and produce factual and impartial interpretive reports. Methods for data collection and analysis that were developed by the USGS have become standard techniques used by numerous Federal, State, and local agencies and by private enterprises. The USGS has implemented a program designed to ensure that all scientific work done by or for USGS Water Science Centers is done in accordance with a quality-assurance plan. The implementation of a groundwater quality-assurance plan will enhance groundwater data collected by the USGS. This report is a quality-assurance plan for groundwater activities conducted by the USGS Dakota Water Science Center and is meant to complement qualityassurance plans for surface-water and water-quality activities and similar plans for the Dakota Water Science Center and general project activities throughout the USGS.

Prioritization of oil and gas fields for regional groundwater monitoring based on a preliminary assessment of petroleum resource development and proximity to California’s groundwater resources

Released July 20, 2018 00:00 EST

2018, Scientific Investigations Report 2018-5065

Tracy Davis, Matthew K. Landon, George L. Bennett

The California State Water Resources Control Board initiated a regional monitoring program in July 2015 to determine where and to what degree groundwater quality may be adversely impacted by oil and gas development activities. A key issue in the implementation of the regional groundwater monitoring program is that each year, detailed characterization work can be done in only a few of California’s 487 onshore oil and gas fields. The first step in monitoring groundwater near petroleum development is to prioritize oil and gas fields using consistent statewide analysis of available data that indicate potential risk of groundwater to oil and gas development.

The U.S. Geological Survey compiled data for four factors that characterize the intensity of petroleum resource development and proximity to groundwater resources: petroleum-well density, volume of water injected in oil fields, vertical proximity of groundwater resources to oil and gas resource development, and water-well density. An overall priority ranking for each field was determined by computing summary metrics, analyzing statewide distributions of summary metrics for all oil and gas fields, using those distributions to define relative categories of potential risk for each factor, and combining relative risk rankings for different factors into an overall priority ranking. This preliminary assessment does not represent an evaluation of groundwater risk to oil and gas development, which needs to be based on detailed analysis and data related to development activities including well stimulation, well integrity issues, produced water ponds, and underground injection.

Based on the prioritization analysis, 22 percent (107 fields) of the total number of oil and gas fields in California were ranked as high priority, 23 percent (114 fields) as moderate priority, and 55 percent (266 fields) as low priority. These results indicate that between 100 and 200 oil fields are principal candidates for the next steps in the regional monitoring program. The land area of fields that ranked high priority accounted for 41 percent of the total field area (3,392 square miles). More than half of the high priority fields were in the southern San Joaquin Valley and the Los Angeles Basin. Some of the larger fields tended to have higher rankings because of greater intensity of petroleum development, sometimes coupled with proximity to groundwater resources.

The U.S. Geological Survey, in collaboration with the California State Water Resources Control Board and other agencies, has begun regional groundwater monitoring near oil and gas fields selected for study through the California Oil, Gas, and Groundwater cooperative program. Groundwater monitoring includes compiling, analyzing, and developing three-dimensional visualizations of existing data, including geological frameworks, salinity mapping, identification of surface features that could potentially affect groundwater quality, locations and depths of oil/gas and water wells, cataloging well-construction integrity issues, and evaluating the directions of groundwater flow. These analyses are required to determine where existing wells should be monitored and where new monitoring wells may need to be drilled.

Assessing the risk of diploid grass carp Ctenopharyngodon idella in the certified triploid supply chain in Ohio

Released July 19, 2018 00:00 EST

2018, Journal of Great Lakes Research

Bryan T. Kinter, Jill A. Jenkins, Jeff T. Tyson

Non-native grass carp (Ctenopharyngodon idella) have been stocked in the United States for vegetation control since the 1970s, and recent evidence suggests some natural reproduction in the Great Lakes basin. Despite all states and provinces bordering Lake Erie either banning grass carp or requiring imports of only sterile, U.S. Fish and Wildlife Service (USFWS)-certified triploids, the majority of grass carp captured and analyzed from Lake Erie are diploid, or reproductively viable. Potential sources of diploid grass carp include illegal importation, compromises in the USFWS-certified triploid shipments, migration from legal diploid states, or natural reproduction resulting from diploid stockings prior to the 1988 Ohio law requiring only certified triploids. The goal of this study was to explore the risk that diploid grass carp occur in the USFWS-certified triploid supply chain destined for Ohio. During 2015 and 2016, undercover Ohio Department of Natural Resources-Division of Wildlife law enforcement purchased 1200 grass carp from 16 distributors, and overnighted 80 dissected grass carp head and eyeball sample shipments (n = 15 fish per shipment) for ploidy analysis by flow cytometry. Standardized methods for both field and laboratory processing were established. No diploid grass carp were detected in these collections, indicating fidelity of the USFWS-certified triploid grass carp supply chain in Ohio. Thus, these shipments are not a likely source of diploid grass carp in Lake Erie. This study is the first large-scale evaluation of the potential for ecological risk from diploid grass carp occurrence in USFSW-certified shipments of triploids for national distribution.

Modeling managed flows in the Sacramento/San Joaquin watershed, California, under scenarios of future change for CASCaDE2

Released July 19, 2018 00:00 EST

2018, Open-File Report 2018-1101

Noah Knowles, Collin Cronkite-Ratcliff

Projections of managed flows from the Sacramento River/San Joaquin River watershed, California, into the San Francisco Bay and Sacramento-San Joaquin Delta under scenarios of future climate change are needed for evaluations of potential impacts on water supply and estuarine ecosystems. A new, multiple-model approach for achieving this is described. First, downscaled global climate model outputs are used to drive an existing Variable Infiltration Capacity/Variable Infiltration Capacity Routing (VIC/RVIC) model of Sacramento/San Joaquin hydrology, resulting in projections of daily, unimpaired flows throughout the watershed. A management model, Computational Assessments of Scenarios of Change for the Delta Ecosystem phase 2 (CASCaDE2) modified CalSim (C2-CalSim), uses these projections as inputs and produces monthly estimates of reservoir and other infrastructure operations and resulting downstream managed flows. A historical resampling algorithm, CASCaDE2 resampling algorithm (CRESPI), also uses the projected daily unimpaired flows, along with historical managed flows, to estimate the daily variability in managed flows throughout the watershed. The monthly and daily managed-flow estimates are combined in a way that preserves the multi-decadal variability and century-scale trends produced by the C2-CalSim model and the day-to-day variability produced by the CRESPI algorithm. The performance of the new modeling approach is evaluated at major inflows to the Bay-Delta estuary using multiple metrics and found to be satisfactory for the purposes of future scenario evaluation.

Near-field receiving-water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California—2017

Released July 19, 2018 00:00 EST

2018, Open-File Report 2018-1107

Daniel J. Cain, Janet K. Thompson, Francis Parchaso, Sarah Pearson, Robin Stewart, Matthew Turner, David Barasch, Ane Slabic, Samuel N. Luoma

Trace-metal concentrations in sediment and in the clam Macoma petalum (formerly reported as Macoma balthica), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, Calif. This report includes the data collected by U.S. Geological Survey (USGS) scientists for the period January 2017 to December 2017. These append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2017 data within the context of the longer, multi-decadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving Water Monitoring Program, initiated in 1994.

Significant reductions in silver and copper concentrations in sediment and M. petalum occurred at the site in the 1980s following the implementation by PARWQCP of advanced wastewater treatment and source control measures. Since the 1990s, concentrations of these elements appear to have stabilized at concentrations somewhat above silver (Ag) or near copper (Cu) regional background concentrations. Data for other metals, including chromium (Cr), mercury (Hg), nickel (Ni), selenium (Se), and zinc (Zn), have been collected since 1994. Over this period, concentrations of these elements have remained relatively constant, aside from seasonal variation that is common to all elements. In 2017, concentrations of silver and copper in M. petalum varied seasonally in response to a combination of site-specific metal exposures and annual growth and reproduction, as reported previously. Seasonal patterns for other elements, including Cr, Ni, Zn, Hg, and Se, were generally similar in timing and magnitude as those for Ag and Cu. This record suggests that legacy contamination and regional-scale factors now largely control sedimentary and bioavailable concentrations of silver and copper, as well as other elements of regulatory interest, at the Palo Alto site.

Analyses of the benthic community structure of a mudflat in south San Francisco Bay over a 40-year period show that changes in the community have occurred concurrent with reduced concentrations of metals in the sediment and in the tissues of the biosentinel clam, M. petalum, from the same area. Analysis of M. petalum shows increases in reproductive activity concurrent with the decline in metal concentrations in the tissues of this organism. Reproductive activity is presently stable (2017), with almost all animals initiating reproduction in the fall and spawning the following spring. The entire infaunal community has shifted from being dominated by several opportunistic species to a community where the species are more similar in abundance, a pattern that indicates a more stable community that is subjected to fewer stressors. In addition, two of the opportunistic species (Ampelisca abdita and Streblospio benedicti) that brood their young and live on the surface of the sediment in tubes have shown a continual decline in dominance coincident with the decline in metals; both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2017. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly in 2011–2012 and returned to pre-2011 numbers in 2017. An unidentified disturbance occurred on the mudflat in early 2008 that resulted in the loss of the benthic animals, except for deep-dwelling animals like M. petalum. However, within two months of this event animals returned to the mudflat. The resilience of the community suggested that the disturbance was not due to a persistent toxin or anoxia. The reproductive mode of most species that were present in 2017 is reflective of species that were available either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2017 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, have pelagic larvae that must survive landing on the sediment, and those that brood their young. USGS scientists view the 2008 disturbance event as a response by the infaunal community to an episodic natural stressor (possibly sediment accretion or a pulse of freshwater), in contrast to the long-term recovery from metal contamination. We will compare this recovery to the long-term recovery observed after the 1970s when the decline in sediment pollutants was the dominating factor.

Geohydrology, geochemistry, and numerical simulation of groundwater flow and land subsidence in the Bicycle Basin, Fort Irwin National Training Center, California

Released July 19, 2018 00:00 EST

2018, Scientific Investigations Report 2018-5067

Jill N. Densmore, Linda R. Woolfenden, Diane L. Rewis, Peter M. Martin, Michelle Sneed, Kevin M. Ellett, Michael Solt, David M. Miller

Groundwater pumping from Bicycle Groundwater Basin (referred to as Bicycle Basin) in the Fort Irwin National Training Center, California, began in 1967. From 1967 to December 2010, about 46,000 acre-feet of water had been pumped from the basin and transported to the Irwin Basin. During this time, not only did water levels in the basin decline by as much as 100 feet, the quality of the groundwater pumped from the basin also deteriorated in some wells. The U.S. Geological Survey collected geohydrologic data from existing wells, test holes, and 16 additional monitoring wells installed at 6 sites in Bicycle Basin during 1992–2011 to determine the quantity and quality of groundwater available in the basin. Geophysical surveys, including electrical, gravity, and seismic refraction surveys, were completed to help determine the geometry of the structural basin, delineate depths to the interface between Quaternary and Tertiary rocks, map the depth to the water table, and used to develop a geohydrologic framework and groundwater-flow model for Bicycle Basin. Water samples were used to determine the groundwater quality in the basin and to delineate potential sources of poor-quality groundwater. Analysis of stable isotopes of oxygen and hydrogen in groundwater indicated that presentday precipitation is not a major source of recharge to the basin. Tritium and carbon-14 data indicated that most of the groundwater in the basin was recharged prior to 1952 and had an apparent age of 15,625–39,350 years. Natural recharge to the basin was not sufficient to replenish the groundwater pumped from the basin. Interferograms from synthetic aperture radar data (InSAR), analyzed to evaluate land-surface subsidence between 1993 and 2010, showed 0.23 to 1.1 feet of subsidence during this period near one production well north of Bicycle Lake (dry) playa. A groundwater-flow model of Bicycle Basin was developed and calibrated using groundwater levels for 1964– 2010, and a subsidence model using land-surface deformation data for 1993–2010. Between January 1967 and December 2010, the simulated total recharge from precipitation runoff and underflow from adjacent basins was about 5,100 acre-feet and pumpage from the Bicycle Basin was about 47,000 acrefeet of water. Total outflows exceeded natural recharge during this period, resulting in a net loss of about 42,100 acre-feet of groundwater storage in the basin. The Fort Irwin National Training Center is considering various groundwater-management options in the Bicycle Basin. The groundwater-flow model was used to (1) evaluate changes in groundwater levels and subsidence with the addition of capture and recharge of simulated runoff in retention basins (scenario 1) for predevelopment through 2010; (2) simulate a base case (scenario 2) for reference; and (3) compare projections of alternative future pumping strategies for 2011–60 (scenarios 3–5). Model results from the runoff-capture simulation (scenario 1) indicated that total recharge, including runoff captured using retention basins, locally increased water levels, which partially offset, but did not mitigate, groundwater depletion associated with pumping. Groundwater-storage depletion in scenario 1 was about 14 percent less than without runoff capture. Simulated-drawdown results in model layer 1 in the eastern part of the basin indicated that, because of the captured runoff, simulated heads were as much as 100 feet higher in December 2010 than prior to the onset of development in 1967. In contrast, simulated drawdown for model without runoff capture indicated that, without captured runoff, simulated heads for December 2010 in this area were 80–90 feet lower than during the predevelopment period. Subsidence was mitigated slightly in scenario 1 compared to without runoff capture; the largest decrease in subsidence at observation sites was about 0.07 feet.

Trends in water quality of selected streams and reservoirs used for water supply in the Triangle area of North Carolina, 1989–2013

Released July 18, 2018 12:30 EST

2018, Scientific Investigations Report 2018-5077

Mary J. Giorgino, Thomas F. Cuffney, Stephen L. Harden, Toby D. Feaster

As the population of the Triangle area in central North Carolina increases, the demand for good quality drinking water from streams and lakes within the upper Neuse and upper Cape Fear River Basins also increases. The Triangle area includes Raleigh, Cary, Research Triangle Park, Durham, Chapel Hill, and the surrounding communities. The U.S. Geological Survey examined temporal trends in water quality for 13 stream and 8 reservoir sites in the two basins on the basis of data collected during 1989–2013. Trends were analyzed using a fitted time-series model that accommodated for shifting trends and variations in streamflow at multiple time scales. Seventeen water-quality properties and constituents were evaluated, including specific conductance and major ions, nutrients, and organic carbon. Suspended solids and suspended sediment were examined at stream sites; chlorophyll a and Secchi transparency were examined at lake sites.

The investigation identified considerable changes in population, land cover, streamflow, and selected water-quality characteristics in the study area over the 25-year period. Specific conductance and concentrations of calcium, magnesium, potassium, sodium, and chloride tended to increase throughout the study area. Area-wide increases were also observed for organic nitrogen. Trends for other water-quality constituents varied on a more site-specific basis because of local watershed influences such as changes to wastewater-treatment processes and substantial shifts from rural to urban land use. Water quality is influenced by multiple, often confounding factors, and thus may change in a non-uniform manner over time. Long-term monitoring is critical for tracking these trends and ensuring resiliency of water supplies for the future. Results from this study may promote the understanding of water-quality response to a growing population and land-cover changes and can assist water-resource managers in the Triangle area in tracking progress toward water-quality goals.

Monitoring the water-quality response of agricultural conservation practices in the Bucks Branch watershed, Sussex County, Delaware, 2014–16

Released July 18, 2018 12:00 EST

2018, Scientific Investigations Report 2018-5020

Judith M. Denver, Alexander M. Soroka, Betzaida Reyes, Todd R. Lester, Deborah A. Bringman, Michael S. Brownley

The purpose of this study was to evaluate the effects of irrigation and cover crops as conservation practices on water quality in groundwater and streams. Bucks Branch, a stream in the Nanticoke River watershed in southwestern Delaware, was identified as having one of the highest concentrations of nitrate in all surface-water sites sampled by the Delaware Department of Natural Resources and Environmental Control (DNREC). The study site is on two adjacent fields bordering Bucks Branch, one that has used irrigation since 2000 and one with dryland farming; both under conservation tillage and long-term rotation of corn, soybean, and small grain crops. A streamgage was installed near the study site fields to measure streamflow and water quality. The study area is typical of farming practices and environmental conditions throughout much of the intensively farmed agricultural land of the Coastal Plain of Delaware and surrounding parts of Maryland. Monitoring was conducted from January 2014 through June 2016. Corn was grown on both fields during the two growing seasons of the study period, and cover crops were planted before or shortly after harvest on both fields. During the second year of data collection, the effects of radish and rye grass cover crops on nutrient transport were studied.

The combined results from data collected for this study show that water and nitrate moved below the root zone year round when soil moisture was high, especially after significant rainfall and frequently after irrigation. Soil water sampled 2 to 3 weeks after nutrients were applied had nitrate concentrations greater than 50 milligrams per liter as nitrogen (mg/L as N) and may be a significant source of nitrate to groundwater. Whereas recharge containing elevated nitrate concentrations also occurred under the dryland field, it was less frequent and of lower concentration than recharge under the irrigated field.

Nitrate was present in all groundwater samples from these sites. Groundwater estimated to have recharged within 10 years or less had higher median concentrations of nitrate than in older water samples. The oldest groundwater encountered was over 30 years old, and had traveled along the longest, deep flowpaths from upland fields to the stream. The median nitrate concentration was 18 mg/L as N in younger water (less than 10 years old) beneath the irrigated field, compared to about 10 mg/L as N in younger water beneath the dryland field. Samples from the shallow upland wells in both study fields showed little, if any, evidence of denitrification. Several samples from deeper wells and from wells near forested riparian zone wetlands that border both fields did show partial denitrification.

A mixing model estimated that between 12 and 22 percent of the nitrate discharging to the stream was lost through uptake and denitrification upstream of the streamgage on Bucks Branch. Continuous data collected at this site and evidence of denitrification in the surface-water samples showed a greater potential for loss of nitrate during the warmer months than the colder months. This pattern was similar to that seen below the streamgage at the most downstream site in the watershed.

A mixed cover crop of radishes and rye was planted prior to removal (radishes) and just after harvest (rye) of the corn crop on the irrigated field. Rye grass was planted shortly after crop harvest on the dryland field. Cover crop biomass samples collected while radishes were growing and after they were killed by freezing temperatures indicates that the early planted radish crop effectively scavenged available nitrogen from the soil. Whereas radish biomass initially held more nitrogen than rye, at 55 to 8 pounds per acre, respectively, leaching of inorganic nitrate following radish die-off was minimal. Soil-water nitrate concentrations during the cover-crop growing period were lower than during the growing season prior to planting of the cover crop. There also was an increase in soil fertility and dissolved organic nitrate in samples of soil water that was likely related to increased soil microbial metabolism. Results indicate that cover crops stored plant nutrients over the winter and did not increase shallow groundwater concentrations of nitrate.

Although conservation practices such as cover crops and nutrient management have been applied to these fields, there was still significant leaching of nitrate to groundwater, especially under the irrigated field. This will likely continue to be a challenge in this area and other parts of the Coastal Plain where soil moisture capacity is relatively low and managing irrigation around rainfall is difficult. Cover crops, when planted in standing corn, are one practice that can effectively pull nitrate from below the root zone to the top layer of soil, thus limiting the amount of potential nitrate leaching to groundwater. Irrigation management that would lower average soil moisture conditions during the growing season also could potentially limit nitrogen transport.

Post-fledging movements and habitat associations of White-tailed Sea Eagles (Haliaeetus albicilla) in Central Asia

Released July 18, 2018 00:00 EST

2018, Wilson Journal of Ornithology

Evgeny A. Bragin, Sharon Poessel, Michael J. Lanzone, Todd Katzner

Behavior of young birds can have important consequences for population dynamics. We investigated the autumnal post-fledging movements of 3 White-tailed Sea Eagles (Haliaeetus albicilla) hatched in Kazakhstan. All 3 eagles traveled south, flying on average 25–108 km/d. Movement was nonrandom, with eagles generally traveling near mosaics of forest, open areas, and water, and rarely using areas with little vegetation. As the first study of movements of White-tailed Sea Eagles in arid Central Asia, this study provides insight into potential limiting factors and how these birds interact with their environment during long-distance movements.

Landsat time series analysis of fractional plant cover changes on abandoned energy development sites

Released July 18, 2018 00:00 EST

2018, International Journal of Applied Earth Observation and Geoinformation (73) 407-419

Eric K. Waller, Miguel Villarreal, Travis Poitras, Travis Nauman, Michael C. Duniway

Oil and natural gas development in the western United States has increased substantially in recent decades as technological advances like horizontal drilling and hydraulic fracturing have made extraction more commercially viable. Oil and gas pads are often developed for production, and then capped, reclaimed, and left to recover when no longer productive. Understanding the rates, controls, and degree of recovery of these reclaimed well sites to a state similar to pre-development conditions is critical for energy development and land management decision processes. Here we use a multi-decadal time series of satellite imagery (Landsat 5, 1984–2011) to assess vegetation regrowth on 365 abandoned well pads located across the Colorado Plateau in Utah, Colorado, and New Mexico. We developed high-frequency time series of the Soil-Adjusted Total Vegetation Index (SATVI) for each well pad using the Google Earth Engine cloud computing platform. BFAST time-series models were used to fit temporal trends, identifying when vegetation was cleared from the site and the magnitudes and rates of vegetation change after abandonment. The time series metrics are used to calculate the relative fractional vegetation cover (RFVC) of each pad, a measure of post-abandonment vegetation cover relative to pre-drilling condition. Mean and median RFVC were 36% (s.d. 33%) and 26%, respectively, five years after abandonment, with one third of well pads having RFVC greater than 50%. Statistical analyses suggest that much of the high vegetation cover is associated with weedy invasive annual species such as cheatgrass (Bromus tectorum) and Russian thistle (Salsola spp.). Climate conditions and the year of abandonment also play a role, with increased cover in later years associated with a wetter period. Non-linear change at many pads suggests longer recovery times than would be estimated by linear extrapolation. New techniques implemented here address a complex response of cover change to soils, management, and climate over time, and can be extended to the operational monitoring of energy development across large areas.

Controls on submarine canyon head evolution: Monterey Canyon, offshore central California

Released July 18, 2018 00:00 EST

2018, Marine Geology (404) 24-40

Katherine L. Maier, Samuel Y. Johnson, Patrick E. Hart

The Monterey submarine canyon, incised across the continental shelf in Monterey Bay, California, provides a record of the link between onshore tectonism, fluvial transport, and deep-marine deposition. High-resolution seismic-reflection imaging in Monterey Bay reveals an extensive paleocanyon unit buried below the seafloor of the continental shelf around Monterey and Soquel canyon heads. Paleocanyons shifted position through numerous phases of cut-and-fill in response to Salinas, Pajaro, and San Lorenzo river extensions and avulsions across the continental shelf during high-frequency Pleistocene sea-level and climatic variations. Five seismic facies within the Monterey paleocanyon unit and below the modern canyon are defined to interpret canyon evolution during the Pleistocene. Repeated sea-level oscillations appear to have switched the main fairway(s) of sediment transport. Large-scale erosion and fill occurred in marine environments. Paleocanyon fill is characterized by paleo-axial channel deposits and mass transport deposits, followed by canyon head abandonment and marine sedimentation. The upper portion of the paleocanyon unit contains relatively small channels that were likely incised by erosion in the paleo-Salinas and Pajaro rivers and filled with a mix of nonmarine and marine deposits. Shifting position of submarine canyons over time is characteristic of Monterey Bay, east of the Monterey Bay Fault Zone, and is likely unidentified in other submarine canyon head regions that lack dense high-resolution seismic-reflection subbottom images. We show that canyon heads can be areas of sediment accumulation linked to sea-level oscillations, providing new insights into submarine canyon evolution and sequence stratigraphy.

Meeting the mineral needs of the United States

Released July 18, 2018 00:00 EST

2018, Eos, Earth and Space Science News

Graham W. Lederer, Erin McCullough

A recent report points out where the United States is most dependent on mineral imports and highlights some ways for reducing this dependence.

Towards coordinated regional multi-satellite InSAR volcano observations: Results from the Latin America pilot project

Released July 18, 2018 00:00 EST

2018, Journal of Applied Volcanology (7)

Matthew Pritchard, Juliet Biggs, Christelle Wauthier, Eugenio Sansosti, David Arnold, Francisco Delgado, Susanna Ebmeier, Scott Henderson, Kristen Stephens, C. Cooper, Kendall Wnuk, Falk Amelung, Victor Rivera Aguilar, Patricia Mothes, Orlando Macedo, Luis E. Lara, Michael Poland, Simona Zoffoli

Within Latin America, about 319 volcanoes have been active in the Holocene, but 202 of these volcanoes have no seismic, deformation or gas monitoring. Following the 2012 Santorini Report on satellite Earth Observation and Geohazards, the Committee on Earth Observation Satellites (CEOS) developed a 4-year pilot project (2013-2017) to demonstrate how satellite observations can be used to monitor large numbers of volcanoes cost-effectively, particularly in areas with scarce instrumentation and/or difficult access. The pilot aims to improve disaster risk management (DRM) by working directly with the volcano observatories that are governmentally responsible for volcano monitoring as well as with the international space agencies (ESA, CSA, ASI, DLR, JAXA, NASA, CNES). The goal is to make sure that the most useful data are collected at each volcano following the guidelines of the Santorini report that observation frequency is related to volcano activity, and to communicate the results to the local institutions in a timely fashion. Here we highlight how coordinated multi-satellite observations have been used by volcano observatories to monitor volcanoes and respond to crises. Our primary tool is measurements of ground deformation made by Interferometric Synthetic Aperture Radar (InSAR), which have been used in conjunction with other observations to determine the alert level at these volcanoes, served as an independent check on ground sensors, guided the deployment of ground instruments, and aided situational awareness. During this time period, we find 26 volcanoes deforming, including 18 of the 28 volcanoes that erupted - those eruptions without deformation were less than 2 on the VEI scale. Another 7 volcanoes were restless and the volcano observatories requested satellite observations, but no deformation was detected. We describe the lessons learned about the data products and information that are most needed by the volcano observatories in the different countries using information collected by questionnaires. We propose a practical strategy for regional to global satellite volcano monitoring for use by volcano observatories in Latin America and elsewhere to realize the vision of the Santorini report.

Secondary hydrogeologic regions of the conterminous United States

Released July 18, 2018 00:00 EST

2018, Groundwater

Elise Watson, Tyler Johnson, Jennifer B. Sharpe, editor(s)

The U.S. Geological Survey (USGS) previously identified and mapped 62 Principal Aquifers (PAs) in the U.S., with 57 located in the conterminous states. Areas outside of PAs, which account for about 40% of the conterminous U.S., were collectively identified as “other rocks.” This paper, for the first time, subdivides this large area into internally-consistent features, defined here as Secondary Hydrogeologic Regions (SHRs). SHRs are areas of other rock within which the rocks or deposits are of comparable age, lithology, geologic or physiographic setting, and relationship to the presence or absence of underling PAs or overlying glacial deposits. A total of 69 SHRs were identified. The number and size of SHRs identified in this paper are comparable to the number and size of PAs previously identified by the USGS. From a two-dimensional perspective, SHRs are complementary to PAs, mapped only where the PAs were not identified on the USGS PA map and not mapped where the PAs were identified. SHRs generally consist of low permeability rocks or deposits, but can include locally productive aquifers. The two maps, taken together, provide a comprehensive, national-scale hydrogeologic framework for assessing and understanding groundwater systems.

The Future: Chapter 12

Released July 18, 2018 00:00 EST

2018, Book chapter, GIS for surface water: Using the National Hydrography Dataset

David L. Blodgett, Alan Rea, Josh Lieberman

Jeffrey D. Simley, editor(s)

No abstract available.

Conservation threats and priorities for raptors across Asia

Released July 18, 2018 00:00 EST

2018, Book chapter, Birds of Prey

Camille B. Conception, Keith L. Bildstein, Nigel J. Collar, Todd Katzner

With long coastlines and some of the world’s most important rivers, mountain ranges, high-altitude plateaus, and islands, Asia is the largest and most populous continent in the world (Lyde 1904; Spencer 1954; Population Reference Bureau 2016). Asia supports all major terrestrial ecosystems and all major climatic types (Galloway et al. 1998; Braimoh and Huang 2015). These include barren ice fields and taigas in North Asia; boreal forests and cold deserts in West, Central, and East Asia; temperate and tropical forests (wet and dry) in East and Southeast Asia; and grasslands in Central and South Asia (Udvardy 1975; Braimoh and Huang 2015). Together, the ecoregions of Asia foster some of the greatest biodiversity on Earth, including six (24%) of 25 global biodiversity hotspots (Myers et al. 2000).

Simulation of potential groundwater recharge for the glacial aquifer system east of the Rocky Mountains, 1980–2011, using the Soil-Water-Balance Model

Released July 18, 2018 00:00 EST

2018, Scientific Investigations Report 2018-5080

Jared J. Trost, Jason L. Roth, Stephen M. Westenbroek, Howard W. Reeves

An understanding of the spatial and temporal extent of groundwater recharge is critical for many types of hydrologic assessments involving water quality, contaminant transport, ecosystem health, and sustainable use of groundwater. Annual potential groundwater recharge was simulated at a 1-kilometer resolution with the Soil-Water-Balance (SWB) model for the glacial aquifer system east of the Rocky Mountains, from central Montana east to Maine, for calendar years 1980–2011. The SWB model used high resolution meteorological, land cover, and soil hydrology datasets that are nationally consistent and publicly available. The SWB model computed daily potential groundwater recharge as precipitation in excess of interception, runoff, evapotranspiration, and soil-water storage capacity. Daily potential recharge values within each year of the simulation were summed to produce annual potential recharge rates. Potential recharge as described in this report is water that infiltrates vertically below the plant rooting zone and is assumed to reach the water table.

The calibrated SWB model in this report is called the glacial SWB model. Model calibration assumed that the area contributing to groundwater discharge equaled the surface watershed. The model was calibrated to stream base flows from 39 watersheds throughout the model domain that had hydrologic conditions appropriate for hydrograph separation. Base flows were calculated from daily streamflow records with the HYSEP local minimum hydrograph separation method The glacial SWB model reproduced the mean annual base-flow calibration targets well; the Nash-Sutcliffe efficiency coefficient was 0.94, and the root mean squared error was 1.28 inches per year.

The glacial SWB model provides insight into the spatial and temporal variability in potential annual recharge across the glacial aquifer system. About 20 percent of the active model area had an average potential recharge rate of less than 1 inch per year. Total precipitation, total recharge, and recharge as a percentage of precipitation increased from west to east. A substantial amount of the recharge water (39 percent) entering the glacial aquifer system travels through developed (urbanized) and agricultural landscapes, which are known to cause water-quality impairments. Regional climatic events, such as the 1988 to 1989 drought, are apparent in the potential recharge time series. Potential recharge generally increased across the glacial aquifer system between 2001 and 2011.

A comparison of the potential recharge from the glacial SWB model to previous broad-scale recharge estimates reveals several important considerations for future SWB modeling applications. Shifts in the overall distribution of potential recharge between separate models can be explained by methods used to generate base-flow calibration target datasets. Spatial patterns in potential recharge simulated by SWB models are strongly dependent on the data and assumptions used to assign model cells to hydrologic soil groups. A review of several SWB models used to estimate groundwater recharge (and not surface runoff) revealed that model results are most sensitive to input climatic data, followed by surface runoff (curve number) and root-zone depth parameters.

Idaho water use, 2015

Released July 18, 2018 00:00 EST

2018, Fact Sheet 2018-3036

Erin M. Murray

The ability to quantify water resources hinges on the understanding of water use by the population. The demand humans place on the water cycle varies across the United States, driven by both need and availability. The U.S. Geological Survey quantifies water use nationally, at the county scale, with estimates of water withdrawals and deliveries, by category of use (for example, irrigation, thermoelectric power, industrial, public supply, including domestic deliveries and self-supply domestic, livestock, mining, and aquaculture) and source (fresh and saline groundwater or surface water) every 5 years. Estimates of water use are an important component of the water budget to help manage water supplies and plan for the future. Understanding water use in Idaho is important not only at the local (county) and State scales, but also at the National level because Idaho ranked third in the Nation for total water use in 2015.

This fact sheet describes calendar year 2015 freshwater withdrawals by source and by each Idaho county. An associated data release provides the data discussed herein. Freshwater withdrawals totaled 17,737 million gallons per day during 2015. Surface water accounted for 70 percent of total withdrawals for all categories of use, mostly for irrigation of crops and aquaculture production. Withdrawals for mining activities were mostly from surface water, whereas the remaining categories of use—public supply, domestic, industrial, livestock, irrigation of golf courses, and thermoelectric power—relied largely on groundwater withdrawals. Most withdrawals occurred in southern Idaho counties to support irrigated agriculture.  

Assessing the effectiveness of riparian restoration projects using Landsat and precipitation data from the cloud-computing application

Released July 17, 2018 00:00 EST

2018, Ecological Engineering (120) 432-440

Mark B. Hausner, Justin L. Huntington, Caroline Nash, Charles Morton, Daniel J. McEvoy, David S. Pilliod, Katherine C. Hegewisch, Britta Daudert, John T. Abatzoglou, Gordon E. Grant

Riparian vegetation along streams provides a suite of ecosystem services in rangelands and thus is the target of restoration when degraded by over-grazing, erosion, incision, or other disturbances. Assessments of restoration effectiveness depend on defensible monitoring data, which can be both expensive and difficult to collect. We present a method and case study to evaluate the effectiveness of restoration of riparian vegetation using a web-based cloud-computing and visualization tool ( to access and process remote sensing and climate data. Restoration efforts on an Eastern Oregon ranch were assessed by analyzing the riparian areas of four creeks that had in-stream restoration structures constructed between 2008 and 2011. Within each study area, we retrieved spatially and temporally aggregated values of summer (June, July, August) normalized difference vegetation index (NDVI) and total precipitation for each water year (October-September) from 1984 to 2017. We established a pre-restoration (1984–2007) linear regression between total water year precipitation and summer NDVI for each study area, and then compared the post-restoration (2012–2017) data to this pre-restoration relationship. In each study area, the post-restoration NDVI-precipitation relationship was statistically distinct from the pre-restoration relationship, suggesting a change in the fundamental relationship between precipitation and NDVI resulting from stream restoration. We infer that the in-stream structures, which raised the water table in the adjacent riparian areas, provided additional water to the streamside vegetation that was not available before restoration and reduced the dependence of riparian vegetation on precipitation. This approach provides a cost-effective, quantitative method for assessing the effects of stream restoration projects on riparian vegetation.

Landscape-scale wildlife species richness metrics to inform wind and solar energy facility siting: An Arizona case study

Released July 17, 2018 00:00 EST

2018, Energy Policy (116) 145-152

Kathryn A. Thomas, Christopher Jarchow, Terry Arundel, Pankaj Jamwal, Amanda Borens, Charles A. Drost

The juxtaposition of wildlife and wind or solar energy facility infrastructure can present problems for developers, planners, policy makers, and management agencies. Guidance on siting of these renewable energy facilities may help identify potential wildlife-facility conflicts with species of regulatory or economic concern. However, existing spatial guidance usually does not consider all wildlife that might use a potential facility location or corridors for its servicing infrastructure. We illustrate an approach toward assessing potential wildlife-facility conflicts using readily available vertebrate habitat models. The U.S. Geological Survey's Gap Analysis Program (GAP) has developed spatial models of potential habitat for vertebrate species across the entire nation. To illustrate their applicability, we used GAP models to estimate richness of all native, terrestrial vertebrates within Arizona and for those vertebrates grouped by class or by sensitivity to the type of facility infrastructure. We examined the spatial overlap of high species richness of each group with agency-developed guidance used to inform facility-siting decisions and found that GAP-based richness mappings augmented existing guidance. As the GAP vertebrate habitat models are publicly available for the entire USA, use of these data can provide a coarse view of potential wildlife-facility conflicts and inform facility planning early in the process.

Turing-style tests for UCERF3 synthetic catalogs

Released July 17, 2018 00:00 EST

2018, Bulletin of the Seismological Society of America (108) 729-741

Morgan T. Page, Nicholas Van Der Elst

Epidemic-Type Aftershock Sequence (ETAS) catalogs generated from the 3rd Uniform California Earthquake Rupture Forecast (UCERF3) model are unique in that they are the first to combine a complex, fault-based long-term forecast with short-term earthquake clustering statistics. We present Turing-style tests to examine whether these synthetic catalogs can successfully imitate observed earthquake behavior in California. We find that UCERF3-ETAS is more spatially diffuse than the observed historic catalog in California and that it is lacking quiet periods that are present in the real catalog. While mean aftershock productivity of the observed catalog is matched closely by UCERF3-ETAS, the real catalog has more inter-sequence productivity variability and small mainshocks have more foreshocks. In sum, we find that UCERF3-ETAS differs from the observed catalog in ways that are foreseeable from its modeling simplifications. The tests we present here can be used on any model which produces suites of synthetic catalogs; as such, in addition to providing avenues for future improvements to the model, they could also be incorporated into testing platforms such as Collaboratory for the Study of Earthquake Predictability (CSEP).

Statistical approach to neural network imaging of karst systems in 3D seismic reflection data

Released July 17, 2018 00:00 EST

2018, Interpretation (6) B15-B35

Daniel Ebuna, Jared W. Kluesner, Kevin J. Cunningham, Joel H. Edwards

The current lack of a robust, standardized technique for geophysical mapping of karst systems can be attributed to both the complexity of the environment and prior technological limitations. Abrupt lateral variations in physical properties that are inherent to karst systems generate significant geophysical noise, challenging conventional seismic signal processing and interpretation. Modern application of neural networks to multi-attribute seismic interpretation now provide a semiautomated method for identifying and leveraging the nonlinear relationships exhibited among seismic attributes. The ambiguity generally associated with designing neural networks for seismic object detection can be reduced via statistical analysis of the extracted attribute data. A data-driven approach to selecting the appropriate set of input seismic attributes, as well as the locations and minimum number of training examples, provides a more objective and computationally efficient method for identifying karst systems using reflection seismology. This statistically optimized neural network technique is thoroughly demonstrated using three-dimensional seismic reflection data collected from the southeastern portion of the Florida carbonate platform. Several dimensionality reduction methods are applied and the resulting karst probability models are evaluated relative to one another based on both quantitative and qualitative criteria. Comparing the preferred model, using quadratic discriminant analysis, to previously available seismic object detection workflows demonstrates the karst-specific nature of the tool. Results suggest that the karst multi-attribute workflow presented is capable of approximating the structural boundaries of karst systems with more accuracy and efficiency than a human counterpart or previously presented seismic interpretation schemes. This objective technique, using solely three-dimensional seismic reflection data, likely represents the most practical approach to mapping karst systems for subsequent hydrogeological modeling.

Applying a Bayesian weighted surveillance approach to detect chronic wasting disease in white‐tailed deer

Released July 17, 2018 00:00 EST

2018, Journal of Applied Ecology

Christopher S. Jennelle, Daniel P. Walsh, Michael D. Samuel, Erik Osnas, Robert E. Rolley, Julia A. Langenberg, Jenny G. Powers, Ryan J. Monello, E. David Demarest, Rolf Gubler, Dennis M. Heisey

  1. Surveillance is critical for early detection of emerging and re‐emerging infectious diseases. Weighted surveillance leverages heterogeneity in infection risk to increase sampling efficiency.
  2. Here, we apply a Bayesian approach to estimate weights for 16 surveillance classes of white‐tailed deer in Wisconsin, USA, relative to hunter‐harvested yearling males. We used these weights to conduct a surveillance programme for detecting chronic wasting disease (CWD) in white‐tailed deer at Shenandoah National Park (SHEN) in Virginia, USA.
  3. Generally, for surveillance, risk of infection increased with age and was greater in males. Clinical suspect deer had the highest risk, with weight estimates of 33.33 and 9.09 for community‐reported and hunter‐reported suspect deer, respectively. Fawns had the lowest risk with an estimated weight of 0.001.
  4. We used surveillance weights for Wisconsin deer to determine sampling effort required to detect a CWD‐positive case in SHEN if prevalence in yearling males ≥0.025. The sampling required to detect CWD was 37–91 adult deer, depending on the adult male:female ratio in the surveillance stream. We collected rectal biopsies from 49 female and 21 male adult deer, and 10 additional samples from vehicle‐killed deer. CWD was not detected and we concluded with 95% probability that prevalence in the reference population (yearling males) was between 0.0% and 3.6%.
  5. Synthesis and applications. Our approach allows managers to estimate relative surveillance weights for different host classes and quantify limits of disease detection in real time when only a sample of animals from a population can be tested, resulting in considerable cost savings for agencies performing wildlife disease detection surveillance. Additionally, it provides a rigorous means of estimating prevalence limits when a disease/pathogen is not detected in a sample set. It is therefore applicable to other wildlife, domestic animal and human disease systems, which can be characterized by surveillance classes with heterogeneous probability of infection. This methodology is also extendable to other disciplines such as invasive species, environmental toxicology, and generally, any ecological question seeking to efficiently use scarce financial and human resources to maximize the detection probability of a rare event.

Soil water dynamics at 15 locations distributed across a desert landscape: insights from a 27‐yr dataset

Released July 17, 2018 00:00 EST

2018, Ecosphere (9) 1-36

Michael C. Duniway, Matthew D. Petrie, Debra P. C. Peters, John P. Anderson, Keith Crossland, Jeffrey E. Herrick

Desert ecosystems are primarily limited by water availability. Within a climatic regime, topography, soil characteristics, and vegetation are expected to determine how the combined effects of precipitation, temperature, and evaporative demand of the atmosphere shape the spatial and temporal patterns of water within the soil profile and across a landscape. To forecast how desert landscapes may respond to future climatic conditions, it is imperative to improve our understanding of these ecohydrologic processes. Here, we report on 27 yr of monthly soil volumetric water content (VWC) measurements and associated soils data from a site in the northern Chihuahuan Desert of North America. The dataset includes VWC and soil properties measured to 3 m in depth across 15 locations that encompass a range of Chihuahuan Desert vegetation types. We use this unique dataset (1) to generate insights into general temporal and depth patterns in VWC, (2) to analyze how VWC corresponds to measures of climatic conditions, and (3) to qualitatively evaluate the relative importance of soils, topographic setting, and vegetation type in mediating temporal patterns in VWC. Analyses of this unique dataset emphasize the importance of soil and topographic setting in determining depth and temporal patterns in VWC across time. Results emphasize the episodic nature of deep wetting events in our study system—essentially limited to three large events over the 27‐yr record driven primarily by wetter than normal winters. Comparison of soil water dynamics between mesquite shrub coppice dunes and interspace soils suggests the “island of fertility” concept does not extend to soil water. Median VWC was strongly coupled to climatic conditions over surprisingly long windows at most locations (6–18 months), suggesting that soil water at depth is decoupled from short climatic pulses. However, VWC dynamics and VWC–climate relationships varied among locations, depths, and seasons, with unexpected similarities in ecohydrologic dynamics observed among very different vegetation types (e.g., an eroded creosote shrubland and a playa grassland). These results further underscore the importance of ecohydrological investigations in these ecosystems, given forecasts for a warmer and more variable climate in deserts globally.