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USGS2006

Comprehensive water quality of the Boulder Creek Watershed, Colorado, during high-flow and low-flow conditions, 2000

Executive Summary The Boulder Creek Watershed, Colorado, is 1160 square kilometers in area and ranges in elevation from 1480 to 4120 meters above sea level. Streamflow originates primarily as snowmelt near the Continental Divide, and thus discharge varies seasonally and annually (Chapter 1). Most of the water in Boulder Creek is diverted for domestic, agricultural, and industrial use. Some diverted water is returned to the creek as wastewater effluent and by ditch returns, and additional water enters as groundwater and by transbasin diversions. These diversions and returns lead to complex temporal and spatial variations in discharge. The variations in discharge, along with natural factors such as geology and climate, and anthropogenic factors such as wastewater treatment, agriculture, mining, and urbanization, can affect water chemistry. As with many watersheds in the American West, dependable water quality and sufficient water supply are issues facing local water managers and users. Detailed water-quality and sediment sampling allows the identification of sources and sinks of chemical constituents and an understanding of the processes at work in a river system. This study, the most comprehensive water-quality analysis performed for Boulder Creek to date, was a cooperative effort of the U.S. Geological Survey (USGS) and the city of Boulder. Geographic information systems and modeling programs were used to delineate watershed boundaries, land cover, and geology (Chapter 2). During high-flow (June 2000) and low-flow (October 2000) conditions, researchers evaluated 226 water-quality variables, including basic water-quality indicators (Chapter 3), major ions and trace elements (Chapter 4), wastewater-derived organic compounds (Chapter 5), and pesticides (Chapter 6). Discharge (Chapter 1) and bed-sediment particle size and mineralogy (Chapter 7) were also evaluated. This cooperative study was facilitated by the Boulder Area Sustainability Information Network (BASIN), which provides public access to environmental information about the Boulder Creek Watershed on a website, www.basin.org. In addition to the USGS and city of Boulder data, researchers at the Institute of Arctic and Alpine Research at the University of Colorado provided water chemistry data for the headwaters of North Boulder Creek, upstream of the reach of the USGS/city of Boulder sampling sites (Chapter 8). Snowmelt produces high flows in Boulder Creek in late spring to early summer (Chapter 1). Because precipitation falling in the headwaters is very dilute (specific conductance about 5 microsiemens per centimeter), most chemical constituents are present in lower concentrations during high flows (Chapters 3, 4, 5, 6, and 8). However, concentrations of some constituents, such as total suspended solids (Chapter 3) and organic carbon (Chapter 5), increase during the spring snowmelt flush. The upper basin, which consists of alpine, subalpine, montane, and foothills regions west of the mouth of Boulder Canyon, is underlain by Precambrian igneous and metamorphic rocks (Chapter 1). Major dissolved inorganic constituents in headwater sites were found to be enriched by factors of 10 to 20 relative to precipitation; this is consistent with minor weathering of the local crystalline bedrock (Chapter 4). Some anthropogenic input is observed in the headwaters; precipitation introduces nitrogen derived from fossil fuel combustion and agricultural activities (Chapter 8). The lower basin, which consists of the plains region east of the mouth of Boulder Canyon, is underlain by Mesozoic sedimentary rock and Quaternary alluvium, and has substantially more anthropogenic sources. Concentrations of most dissolved inorganic constituents increased in the lower basin. Differentiation between natural and anthropogenic sources of some dissolved constituents is difficult because both sources contribute to the water composition in this region. The increase of most major constituents (bicarbonate, calcium, chloride, magnesium, sodium, and sulfate) is consistent with weathering of the underlying sedimentary bedrock (Chapter 4). It is likely that anthropogenic loading of constituents in this reach occurs during storm events. Fecal coliform concentrations were variable and in some cases exceeded state standards, primarily during low-flow conditions (Chapter 3). Effluent from Boulder’s 75th Street Wastewater Treatment Plant (WWTP) has a substantial impact on the water chemistry of lower Boulder Creek. The WWTP increases the concentrations of nutrients such as nitrogen and phosphorus (Chapter 3), major ions and trace metals (Chapter 4), and organic carbon (Chapter 5) in Boulder Creek. The effluent contained a spike in gadolinium, a rare earth element that is ingested for magnetic resonance imaging as a contrasting agent and then excreted to the urban wastewater system. The effluent also contained trace organic compounds such as surfactants, pharmaceuticals, hormones (Chapter 5), and pesticides (Chapter 6), which also were detected at downstream Boulder Creek sites. Water chemistry of Boulder Creek downstream of the WWTP is largely controlled by the degree of dilution of the wastewater effluent, which varies depending on the baseflow of Boulder Creek, the volume of wastewater effluent, and depletion by agricultural diversions. Coal Creek, a tributary of Boulder Creek, contains wastewater effluent from four additional WWTPs, and increases the load of many constituents in Boulder Creek. In addition to the impact from wastewater effluent, lower Boulder Creek is affected by agricultural land use. Eleven of 84 analyzed pesticides were detected in Boulder Creek or its inflows, primarily in the eastern section of the watershed (Chapter 6). This collaborative study provides an in-depth evaluation of the hydrology, water chemistry, and sediment mineralogy of North Boulder Creek, Middle Boulder Creek, Boulder Creek, and major inflows. The detailed sampling and analysis in this report provide a baseline for future reference, as well as information on the effect of land use and geology on water chemistry.

Colorado↗

USGS2020

The Long-term effect of bleeding for Limulus amebocyte lysate on annual survival and recapture of tagged horseshoe crabs

In the U.S., 525,000 horseshoe crabs ( Limulus polyphemus ) per year have been captured during 2013–2017, brought to biomedical facilities, and bled to produce Limulus amebocyte lysate (LAL), then mostly released to the area of capture. The Atlantic States Marine Fisheries Commission estimates short-term bleeding-induced mortality to be 15% (4% to 30%), resulting in mortality of approximately 78,750 horseshoe crabs annually in recent years comprising a minor portion (<13%) of the up to one million annual coastwide landings dominated by harvest for bait. However, the long-term effect of bleeding for LAL on annual survival and spawning behavior is unknown; thus, results from short-term studies alone might underestimate bleeding effects at the population level. To address this knowledge gap, we analyzed data from the U.S. Fish and Wildlife horseshoe crab tagging database to estimate the differences in survival and recapture rates of bled and not bled horseshoe crabs tagged in the same years and geographic area. Contrary to expectation, survival was not lower for bled crabs compared to unbled crabs. Differences varied, but survival estimates tended to be higher for bled crabs than for unbled crabs. However, biomedical culling and selection for younger or healthier animals could have resulted in biomedically tagged individuals representing a healthier subset of the overall population with subsequent higher survival. Furthermore, the tagging analysis revealed a post-bleeding reduction in capture probability, which could indicate decreased spawning activity, evident in males more than females. Continued tagging of bled and unbled crabs in the same geographic area while recording age class and sex will contribute to the further resolution of LAL production’s effect on horseshoe crab populations.

Delaware, Maryland, New Jersey, Virginia↗

USGS2013

Location-only and use-availability data: analysis methods converge

This Special Feature arose from a session on a topic of the same name that took place during The Wildlife Society meeting in Kona, Hawaii, from 5 to 10 November, 2011. The purpose of that session and this Special Feature is to compare methods for predictive modelling of species geographical distributions and the modelling of habitat (resource) selection by animals. The predictive modelling of species geographical distributions and the modelling of habitat selection based on the environmental conditions at sites where animals are known to occur are essentially the same problem. Presence-only and used-available data both consist of a sample of locations with known presence of a species or an individual. A separate sample of locations from a study area, with unknown presence (pseudo-absence), is also assumed to exist. The probability or relative probability of presence of a species or individual is modelled and estimated across a certain time implicitly defined by the sampling mechanism, for example, by the time period during which museum specimens or radiotelemetry data were collected. A number of modelling methods have appeared in the literature over the last couple of decades. Many of these methods were made feasible by the availability of geographical information systems (GIS), global positioning system (GPS) radiotelemetry and public online data access initiatives (e.g. global biodiversity information facility). The papers in this Special Feature are intended to present the state of the methodological art in their subject area, with particular attention paid to contrasting the advantages and disadvantages of alternative methods of analysis for data.

Journal of Animal Ecology↗

USGS2015

Changes in seasonality and timing of peak streamflow in snow and semi-arid climates of the north-central United States, 1910–2012

Changes in the seasonality and timing of annual peak streamflow in the north-central USA are likely because of changes in precipitation and temperature regimes. A source of long-term information about flood events across the study area is the U.S. Geological Survey peak streamflow database. However, one challenge of answering climate-related questions with this dataset is that even in snowmelt-dominated areas, it is a mixed population of snowmelt/spring rain generated peaks and summer/fall rain generated peaks. Therefore, a process was developed to divide the annual peaks into two populations, or seasons, snowmelt/spring, and summer/fall. The two series were then tested for the hypotheses that because of changes in precipitation regimes, the odds of summer/fall peaks have increased and, because of temperature changes, snowmelt/spring peaks happen earlier. Over climatologically and geographically similar regions in the north-central USA, logistic regression was used to model the odds of getting a summer/fall peak. When controlling for antecedent wet and dry conditions and geographical differences, the odds of summer/fall peaks occurring have increased across the study area. With respect to timing within the seasons, trend analysis showed that in northern portions of the study region, snowmelt/spring peaks are occurring earlier. The timing of snowmelt/spring peaks in three regions in the northern part of the study area is earlier by 8.7– 14.3 days. These changes have implications for water interests, such as potential changes in lead-time for flood forecasting or changes in the operation of flood-control dams.

Colorado, Iowa, Kansas, Minnesota, Missouri, Monta↗

USGS2004

Barrier island morphodynamic classification based on lidar metrics for north Assateague Island, Maryland

In order to reap the potential of airborne lidar surveys to provide geological information useful in understanding coastal sedimentary processes acting on various time scales, a new set of analysis methods are needed. This paper presents a multi-temporal lidar analysis of north Assateague Island, Maryland, and demonstrates the calculation of lidar metrics that condense barrier island morphology and morphological change into attributed linear features that may be used to analyze trends in coastal evolution. The new methods proposed in this paper are also of significant practical value, because lidar metric analysis reduces large volumes of point elevations into linear features attributed with essential morphological variables that are ideally suited for inclusion in Geographic Information Systems. A morphodynamic classification of north Assategue Island for a recent 10 month time period that is based on the recognition of simple patterns described by lidar change metrics is presented. Such morphodynamic classification reveals the relative magnitude and the fine scale alongshore variation in the importance of coastal changes over the study area during a defined time period. More generally, through the presentation of this morphodynamic classification of north Assateague Island, the value of lidar metrics in both examining large lidar data sets for coherent trends and in building hypotheses regarding processes driving barrier evolution is demonstrated

Maryland↗

USGS2003

Cartographic services contract...for everything geographic

The U.S. Geological Survey's (USGS) Cartographic Services Contract (CSC) is used to award work for photogrammetric and mapping services under the umbrella of Architect-Engineer (A&E) contracting. The A&E contract is broad in scope and can accommodate any activity related to standard, nonstandard, graphic, and digital cartographic products. Services provided may include, but are not limited to, photogrammetric mapping and aerotriangulation; orthophotography; thematic mapping (for example, land characterization); analog and digital imagery applications; geographic information systems development; surveying and control acquisition, including ground-based and airborne Global Positioning System; analog and digital image manipulation, analysis, and interpretation; raster and vector map digitizing; data manipulations (for example, transformations, conversions, generalization, integration, and conflation); primary and ancillary data acquisition (for example, aerial photography, satellite imagery, multispectral, multitemporal, and hyperspectral data); image scanning and processing; metadata production, revision, and creation; and production or revision of standard USGS products defined by formal and informal specification and standards, such as those for digital line graphs, digital elevation models, digital orthophoto quadrangles, and digital raster graphics.

Fact Sheet↗

USGS2007

Rapid Data Delivery System (RDDS)

Since the start of the active 2000 summer fire season, the U. S. Geological Survey (USGS) Rocky Mountain Geographic Science Center (RMGSC) has been actively engaged in providing crucial and timely support to Federal, State, and local natural hazards monitoring, analysis, response, and recovery activities. As part of this support, RMGSC has developed the Rapid Data Delivery System (RDDS) to provide emergency and incident response teams with timely access to geospatial data. The RDDS meets these needs by combining a simple web-enabled data viewer for the selection and preview of vector and raster geospatial data with an easy to use data ordering form. The RDDS viewer also incorporates geospatial locations for current natural hazard incidents, including wildfires, earthquakes, hurricanes, and volcanoes, allowing incident responders to quickly focus on their area of interest for data selection.

Fact Sheet↗

USGS2008

The National Map product and services directory

As one of the cornerstones of the U.S. Geological Survey's (USGS) National Geospatial Program (NGP), The National Map is a collaborative effort among the USGS and other Federal, state, and local partners to improve and deliver topographic information for the Nation. It has many uses ranging from recreation to scientific analysis to emergency response. The National Map is easily accessible for display on the Web, as products, and as downloadable data. The geographic information available from The National Map includes orthoimagery (aerial photographs), elevation, geographic names, hydrography, boundaries, transportation, structures, and land cover. Other types of geographic information can be added to create specific types of maps. Of major importance, The National Map currently is being transformed to better serve the geospatial community. The USGS National Geospatial Program Office (NGPO) was established to provide leadership for placing geographic knowledge at the fingertips of the Nation. The office supports The National Map , Geospatial One-Stop (GOS), National Atlas of the United States ® , and the Federal Geographic Data Committee (FGDC). This integrated portfolio of geospatial information and data supports the essential components of delivering the National Spatial Data Infrastructure (NSDI) and capitalizing on the power of place.

Fact Sheet↗

USGS2019

US Topo Product Standard

This document defines a U.S. Geological Survey (USGS) digital topographic map. This map product series, named “US Topo,” is modeled on the now historical USGS 7.5-minute (1:24,000 scale) topographic map series produced and printed by the USGS from 1947 to 2006. US Topo maps have the same extent, scale, and general layout as the historical topographic maps. US Topo maps incorporate an orthorectified image (hereinafter referred to as “orthoimage”) and shaded relief image along with a selection of data that were included in the historical 7.5-minute topographic maps. Between June and September of 2017, the USGS transitioned the format of US Topo maps to be published, by using a geospatial extension, in an International Organization for Standardization (ISO) 32000-compliant Adobe® portable document format (PDF) that is called a “geospatial PDF.” Previously, US Topo maps were published, by using geospatial extensions patented by TerraGo® Technologies, in PDF in a format called a “GeoPDF®.” The geospatial PDF design allows a user to zoom in and out in a georeferenced environment, turn layers on and off, view or print any combination of layers, and print any portion of the map at the published scale. US Topo maps are intended to serve conventional map users by providing geographic information system (GIS) information in symbolized form in the customary topographic map layout. The maps are not intended for advanced GIS analysis applications. These products are built on standard coordinate systems and include full U.S. National Grid (USNG) lines, making US Topo maps particularly useful for emergency first-response operations. These maps are also used by traditional topographic map users, such as resource managers, planners, and recreational users who continue to have a need for the symbolized feature data contained in the 7.5-minute quadrangle maps. Full-size style sheet templates in PDF defining the placement of map elements, marginalia, and font sizes and styles accompany this standard. US Topo maps published as geospatial PDFs are fashioned to conform to these style sheets so that a user can print out a map at the 1:24,000, 1:25,000, or 1:20,000 scale using the dimensions of the traditional standard 7.5-minute quadrangle. Symbology and type specifications for feature content and detailed requirements for geospatial content will be published separately. This document is an update of the US Topo Product Standard published in 2011 (Cooley and others, 2011). It is applicable to all US Topo maps. Updates in this version include the introduction of an ISO 32000-compliant geospatial PDF as a new file format for published maps; new style sheet templates for 1:24,000-scale maps (conterminous United States and Hawaii), 1:25,000-scale maps (Alaska), and 1:20,000-scale maps (Puerto Rico and U.S. Virgin Islands); an updated US Topo Map Symbol attachment; minor updates to text, including changes to the features and layers included in the US Topo product and the sheet size of the US Topo maps; updated figures demonstrating the US Topo product; an updated metadata file containing map-specific information.

Techniques and Methods↗

USGS2003

Estimating water temperatures in small streams in western Oregon using neural network models

Artificial neural network models were developed to estimate water temperatures in small streams using data collected at 148 sites throughout western Oregon from June to September 1999. The sites were located on 1st-, 2nd-, or 3rd-order streams having undisturbed or minimally disturbed conditions. Data collected at each site for model development included continuous hourly water temperature and description of riparian habitat. Additional data pertaining to the landscape characteristics of the basins upstream of the sites were assembled using geographic information system (GIS) techniques. Hourly meteorological time series data collected at 25 locations within the study region also were assembled. Clustering analysis was used to partition 142 sites into 3 groups. Separate models were developed for each group. The riparian habitat, basin characteristic, and meteorological time series data were independent variables and water temperature time series were dependent variables to the models, respectively. Approximately one-third of the data vectors were used for model training, and the remaining two-thirds were used for model testing. Critical input variables included riparian shade, site elevation, and percentage of forested area of the basin. Coefficient of determination and root mean square error for the models ranged from 0.88 to 0.99 and 0.05 to 0.59 oC, respectively. The models also were tested and validated using temperature time series, habitat, and basin landscape data from 6 sites that were separate from the 142 sites that were used to develop the models. The models are capable of estimating water temperatures at locations along 1st-, 2nd-, and 3rd-order streams in western Oregon. The model user must assemble riparian habitat and basin landscape characteristics data for a site of interest. These data, in addition to meteorological data, are model inputs. Output from the models include simulated hourly water temperatures for the June to September period. Adjustments can be made to the shade input data to simulate the effects of minimum or maximum shade on water temperatures.

Water-Resources Investigations Report↗

USGS1984

Evolution of the MOSS geographic information system for 32-bit computer systems

The authors discuss the current status and plans regarding the 32-bit implementation of the Map Overly and Statistical System (MOSS) geographic information system. Increasing interest in this system is promoting significant expansion of its capabilities, but any such enhancements will require careful analysis and planning to ensure that the resulting system is functionally complete and efficient yet flexible enough to adapt to a variety of user requirements and systems. All enhancements must be coordinated among centers of development in order to ensure the continued viability of a single MOSS. A baseline software configuration must be defined, and procedures must be developed to ensure coordination of any modifications to the baseline. Finally, there is significant interest in maintaining the public-domain aspects of MOSS to promote its shared use in the Department of the Interior. For these reasons, coordination efforts such as those initiated by the IDCCC and the MOSS Users Workshop should be strongly supported by the MOSS user community.

Conference Paper↗

USGS2011

The Regionalization of National-Scale SPARROW Models for Stream Nutrients

This analysis modifies the parsimonious specification of recently published total nitrogen (TN) and total phosphorus (TP) national‐scale SPAtially Referenced Regressions On Watershed attributes models to allow each model coefficient to vary geographically among three major river basins of the conterminous United States. Regionalization of the national models reduces the standard errors in the prediction of TN and TP loads, expressed as a percentage of the predicted load, by about 6 and 7%. We develop and apply a method for combining national‐scale and regional‐scale information to estimate a hybrid model that imposes cross‐region constraints that limit regional variation in model coefficients, effectively reducing the number of free model parameters as compared to a collection of independent regional models. The hybrid TN and TP regional models have improved model fit relative to the respective national models, reducing the standard error in the prediction of loads, expressed as a percentage of load, by about 5 and 4%. Only 19% of the TN hybrid model coefficients and just 2% of the TP hybrid model coefficients show evidence of substantial regional specificity (more than ±100% deviation from the national model estimate). The hybrid models have much greater precision in the estimated coefficients than do the unconstrained regional models, demonstrating the efficacy of pooling information across regions to improve regional models.

Journal of the American Water Resources Associatio↗

USGS2024

Ticks without borders: Microbiome of immature neotropical tick species parasitizing migratory songbirds along northern Gulf of Mexico

Introduction: The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can cause the emergence of novel tick-borne pathogens. This study examined the prevalence of exotic tick species parasitizing migratory songbirds at stopover sites along the northern Gulf of Mexico using the mitochondrial 12S rRNA gene. Methods: Overall, 421 individual ticks in the genera Amblyomma , Haemaphysalis , and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre were the most abundant tick genera and species, respectively. A high throughput 16S ribosomal RNA sequencing approach characterized the microbial communities and identified pathogenic microbes in all tick samples. Results and discussion: Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant pathogens were Rickettsia and endosymbiont Francisella , Candidatus Midichloria , and Spiroplasma . Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also noted a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium . Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing mean dispersal distances from 421–5003 kilometers. These findings spotlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.

Alabama, Louisiana↗

USGS2021

Range-wide declines of northern spotted owl populations in the Pacific Northwest: A meta-analysis

The northern spotted owl ( Strix occidentalis caurina ) inhabits older coniferous forests in the Pacific Northwest and has been at the center of forest management issues in this region. The immediate threats to this federally listed species include habitat loss and competition with barred owls ( Strix varia ), which invaded from eastern North America. We conducted a prospective meta-analysis to assess population trends and factors affecting those trends in northern spotted owls using 26 years of survey and capture-recapture data from 11 study areas across the owls' geographic range to analyze demographic traits, rates of population change, and occupancy parameters for spotted owl territories. We found that northern spotted owl populations experienced significant declines of 6–9% annually on 6 study areas and 2–5% annually on 5 other study areas. Annual declines translated to ≤35% of the populations remaining on 7 study areas since 1995. Barred owl presence on spotted owl territories was the primary factor negatively affecting apparent survival, recruitment, and ultimately, rates of population change. Analysis of spotted and barred owl detections in an occupancy framework corroborated the capture-recapture analyses with barred owl presence increasing territorial extinction and decreasing territorial colonization of spotted owls. While landscape habitat components reduced the effect of barred owls on these rates of decline, they did not reverse the negative trend. Our analyses indicated that northern spotted owl populations potentially face extirpation if the negative effects of barred owls are not ameliorated while maintaining northern spotted owl habitat across their range.

California, Oregon, Washington↗

USGS2013

A GIS and statistical approach to identify variables that control water quality in hydrothermally altered and mineralized watersheds, Silverton, Colorado, USA

Hydrothermally altered bedrock in the Silverton mining area, southwest Colorado, USA, contains sulfide minerals that weather to produce acidic and metal-rich leachate that is toxic to aquatic life. This study utilized a geographic information system (GIS) and statistical approach to identify watershed-scale geologic variables in the Silverton area that influence water quality. GIS analysis of mineral maps produced using remote sensing datasets including Landsat Thematic Mapper, advanced spaceborne thermal emission and reflection radiometer, and a hybrid airborne visible infrared imaging spectrometer and field-based product enabled areas of alteration to be quantified. Correlations between water quality signatures determined at watershed outlets, and alteration types intersecting both total watershed areas and GIS-buffered areas along streams were tested using linear regression analysis. Despite remote sensing datasets having varying watershed area coverage due to vegetation cover and differing mineral mapping capabilities, each dataset was useful for delineating acid-generating bedrock. Areas of quartz–sericite–pyrite mapped by AVIRIS have the highest correlations with acidic surface water and elevated iron and aluminum concentrations. Alkalinity was only correlated with area of acid neutralizing, propylitically altered bedrock containing calcite and chlorite mapped by AVIRIS. Total watershed area of acid-generating bedrock is more significantly correlated with acidic and metal-rich surface water when compared with acid-generating bedrock intersected by GIS-buffered areas along streams. This methodology could be useful in assessing the possible effects that alteration type area has in either generating or neutralizing acidity in unmined watersheds and in areas where new mining is planned.

Colorado↗

USGS2011

A novel member of the family Hepeviridae from cutthroat trout ( Oncorhynchus clarkii )

Beginning in 1988, the Chinook salmon embryo (CHSE-214) cell line was used to isolate a novel virus from spawning adult trout in the state of California, USA. Termed the cutthroat trout ( Oncorhynchus clarkii ) virus (CTV), the small, round virus was not associated with disease, but was subsequently found to be present in an increasing number of trout populations in the western USA, likely by a combination of improved surveillance activities and the shipment of infected eggs to new locations. Here, we report that the full length genome of the 1988 Heenan Lake isolate of CTV consisted of 7269 nucleotides of positive-sense, single-stranded RNA beginning with a 5' untranslated region (UTR), followed by three open reading frames (ORFs), a 3' UTR and ending in a polyA tail. The genome of CTV was similar in size and organization to that of Hepatitis E virus (HEV) with which it shared the highest nucleotide and amino acid sequence identities. Similar to the genomes of human, rodent or avian hepeviruses, ORF 1 encoded a large, non-structural polyprotein that included conserved methyltransferase, protease, helicase and polymerase domains, while ORF 2 encoded the structural capsid protein and ORF 3 the phosphoprotein. Together, our data indicated that CTV was clearly a member of the family Hepeviridae , although the level of amino acid sequence identity with the ORFs of mammalian or avian hepeviruses (13-27%) may be sufficiently low to warrant the creation of a novel genus. We also performed a phylogenetic analysis using a 262. nt region within ORF 1 for 63 isolates of CTV obtained from seven species of trout reared in various geographic locations in the western USA. While the sequences fell into two genetic clades, the overall nucleotide diversity was low (less than 8.4%) and many isolates differed by only 1-2 nucleotides, suggesting an epidemiological link. Finally, we showed that CTV was able to form persistently infected cultures of the CHSE-214 cell line that may have use in research on the biology or treatment of hepevirus infections of humans or other animals.

Virus Research↗

USGS1992

A statistical overview of mass movement characteristics on the North American Atlantic outer continental margin

An analysis of 179 mass movements on the North American Atlantic continental slope and upper rise shows that slope failures have occurred throughout the geographic extent of the outer margin. Although the slope failures show no striking affinity for a particular depth as an origination level, there is a broad, primary mode centered at about 900 m. The resulting slides terminate at almost all depths and have a primary mode at 1100 m, but the slope/rise boundary (at 2200 m) also is an important mode. Slope failures have occurred at declivities ranging from 1° to 30° (typically, 4°); the resultant mass movement deposits vary in width from 0.2 to 50 km (typically, 1–2 km) and in length from 0.3 to 380 km (typically, 2–4 km), and they have been reported to be as thick as 650 m. On a numeric basis, mass movements are slightly more prevalent on open slopes than in other physiographic settings, and both translational and rotational failure surfaces are common. The typical mass movement is disintegrative in nature. Open slope slides tend to occur at lower slope angles and are larger than canyon slides. Further, large‐scale slides rather than small‐scale slides tend to originate on gentle slopes (≍ 3–4°). Rotational slope failures appear to have a slightly greater chance of occurring in canyons, but there is no analogous bias associated with translational failures. Similarly, disintegrative slides seem more likely to be associated with rotational slope failures than translational ones and are longer than their nondisintegrative counterparts. The occurrence of such a variety of mass movements at low declivities implies that a regional failure mechanism has prevailed. We suggest that earthquakes or, perhaps in some areas, gas hydrates are the most likely cause of the slope failures.

Marine Geotechnology↗

USGS2021

Precipitation-runoff processes in the Merced River Basin, Central California, with prospects for streamflow predictability, water years 1952–2013

The U.S. Geological Survey, in cooperation with the California Department of Water Resources (DWR), has constructed a new spatially detailed Precipitation-Runoff Modeling System (PRMS) model for the Merced River Basin, California, which is a tributary of the San Joaquin River in California. Operated through an Object User Interface (OUI) with Ensemble Streamflow Prediction (ESP) and daily climate distribution preprocessing functionality, the model is calibrated primarily to simulate (and eventually, forecast) year-to-year variations of inflows to Lake McClure during the critical April–July snowmelt season. The model is intended to become part of a suite of methods used by DWR for estimating daily streamflow from the Merced River Basin, especially during the snowmelt season. This study describes the results of the application of an analysis tool that simulates responses to climate and land-use variations at a higher spatial resolution than previously available to DWR. A geographic information system was used to delineate the model domain, that is, areas draining to a single outlet at U.S. Geological Survey streamflow-gaging station 11270900, Merced River below Merced Falls Dam, near Snell, CA (also known as California Data Exchange Center station MRC), and subdrainage areas, including four draining to internal gages used as calibration targets. Using this delineation, three contiguous subbasins were recognized and, along with the model domain and nested calibration targets, are the simulation units evaluated in this report. An auto-calibration tool, LUCA (Let Us CAlibrate), was used for each calibration node, from headwaters to basin outlet, and then parameters were manually adjusted to complete the calibration. The main objective was to match April–July snowmelt seasonal discharge values of simulated streamflow to observed (measured or reconstructed) discharge values. Calibration or validation periods used site-specific streamflows—mostly from October 1, 1988, through September 30, 2013—but differed according to the period-of-record available for the measurements collected at internal gages or reconstructed flows for the single outlet. The accuracy of the Merced PRMS streamflow simulations varied seasonally, as compared to observed values. Based on statistical results, the Merced PRMS model satisfactorily simulated snowmelt seasonal streamflows. April–July calibrations for all areas had small negative bias (not greater than 7 percent) and low relative error (less than 8 percent). Less satisfactory performance for other seasons was attributed to several factors: (1) high uncertainty in low or zero flows in summer and fall, (2) lack of accounting for basin withdrawals and anthropogenic water use, (3) unavailability and (or) inaccuracy of observed (measured) meteorological input data, and (4) uncertainty in reconstructed streamflow data. With some additional refinement, the Merced PRMS model may be used for forecasting seasonal and longer-term streamflow variations; evaluating forecasted and past climate and land cover changes; providing water-resource managers with a consistent and documented method for estimating streamflow at ungaged sites within the basin; and aiding environmental studies, hydraulic design, water management, and water-quality projects in the Merced River Basin.

California↗