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Case definitions for wildlife diseases

Welcome to the first manual of “Case Definitions for Wildlife Diseases,” a “living” electronic publication. The plan is to add and update this manual’s case definitions periodically as warranted; thus, this manual will never be completed, and readers should download the latest versions of specific chapters (that is, definitions) when available. Constructive suggestions from readers are welcome and will help guide adjustments as this project progresses. The purpose of this manual is to provide case definitions for selected diseases of importance to wildlife in Canada and the United States. Case definitions provide standard sets of criteria for classifying the degree of certainty of a particular diagnosis and help improve surveillance data quality and comparability. Better data and standardization allow for improved data sharing, which increases geographic and species surveillance coverage and permits more robust analyses. The definitions included in this manual have been developed by veterinary pathologists, epidemiologists, and wildlife biologists primarily from the U.S. Geological Survey National Wildlife Health Center (NWHC) and Canadian Wildlife Health Cooperative (CWHC). Pathologists from each organization reviewed and finalized the definitions. Each case definition has been peer reviewed by two scientific experts before publication. This manual begins with the case definition template. This generic template includes four sections: “Individual, Place, and Time Criteria for Diagnosis and Testing,” “Field Criteria for Diagnosis,” “Laboratory Criteria for Diagnosis,” and “Epidemiological Linkage Criteria for Diagnosis” and can be used to guide development of new case definitions. Information in each section is then combined to provide an overall case classification. Disease diagnoses are classified as “Confirmed,” “Presumptive,” or “Suspected;” and evidence of a pathogen or toxin is classified as “Exposed” or “Present/Detected.” Each subsequent chapter is then a case definition for a specific disease of wildlife, and infectious and non-infectious diseases are included.

Techniques and Methods↗

Carbonate margin, slope, and basin facies of the Lisburne Group (Carboniferous-Permian) in northern Alaska

The Lisburne Group (Carboniferous-Permian) consists of a carbonate platform that extends for >1000 km across northern Alaska, and diverse margin, slope, and basin facies that contain world-class deposits of Zn and Ba, notable phosphorites, and petroleum source rocks. Lithologic, paleontologic, isotopic, geochemical, and seismic data gathered from outcrop and subsurface studies during the past 20 years allow us to delineate the distribution, composition, and age of the off-platform facies, and to better understand the physical and chemical conditions under which they formed. The southern edge of the Lisburne platform changed from a gently sloping, homoclinal ramp in the east to a tectonically complex, distally steepened margin in the west that was partly bisected by the extensional Kuna Basin (~200 by 600 km). Carbonate turbidites, black mudrocks, and radiolarian chert accumulated in this basin; turbidites were generated mainly during times of eustatic rise in the late Early and middle Late Mississippian. Interbedded black mudrocks (up to 20 wt% total organic carbon), granular and nodular phosphorite (up to 37 wt% P 2 O 5 ), and fine-grained limestone rich in radiolarians and sponge spicules formed along basin margins during the middle Late Mississippian in response to a nutrient-rich, upwelling regime. Detrital zircons from a turbidite sample in the western Kuna Basin have mainly Neoproterozoic through early Paleozoic U-Pb ages (~900-400 Ma), with subordinate populations of Mesoproterozoic and late Paleoproterozoic grains. This age distribution is similar to that found in slightly older rocks along the northern and western margins of the basin. It also resembles age distributions reported from Carboniferous and older strata elsewhere in northwestern Alaska and on Wrangel Island. Geochemical and isotopic data indicate that suboxic, denitrifying conditions prevailed in the Kuna Basin and along its margins. High V/Mo, Cr/Mo, and Re/Mo ratios (all marine fractions [MF]) and low MnO contents (<0.01 wt%) characterize Lisburne black mudrocks. Low Qmf/Vmf ratios (mostly 0.8-4.0) suggest moderately to strongly denitrifying conditions in suboxic bottom waters during siliciclastic and phosphorite sedimentation. Elevated to high Mo contents (31-135 ppm) in some samples are consistent with seasonal to intermittent sulfidic conditions in bottom waters, developed mainly along the basin margin. High d 15 N values (6-120) imply that the waters supplying nutrients to primary producers in the photic zone had a history of denitrification either in the water column or in underlying sediments. Demise of the Lisburne platform was diachronous and reflects tectonic, eustatic, and environmental drivers. Southwestern, south-central, and northwestern parts of the platform drowned during the Late Mississippian, coincident with Zn and Ba metallogenesis within the Kuna Basin and phosphogenesis along basin margins. This drowning was temporary (except in the southwest) and likely due to eutrophication associated with upwelling and sea-level rise enhanced by regional extension, which allowed suboxic, denitrifying waters to form on platform margins. Final drowning in the southcentral area occurred in the Early Pennsylvanian and also may have been linked to regional extension. In the northwest, platform sedimentation persisted into the Permian; its demise there appears to have been due to increased siliciclastic input. Climatic cooling may have produced additional stress on parts of the Lisburne platform biota during Pennsylvanian and Permian times.

Alaska↗

Porphyry copper assessment of Southeast Asia and Melanesia: Chapter D in Global mineral resource assessment

The U.S. Geological Survey collaborated with member countries of the Coordinating Committee for Geoscience Programmes in East and Southeast Asia (CCOP) on an assessment of the porphyry copper resources of Southeast Asia and Melanesia as part of a global mineral resource assessment. The region hosts world-class porphyry copper deposits and underexplored areas that are likely to contain undiscovered deposits. Examples of known porphyry copper deposits include Batu Hijau and Grasberg in Indonesia; Panguna, Frieda River, and Ok Tedi in Papua New Guinea; and Namosi in Fiji. This assessment covers the countries of Cambodia, Indonesia, Lao People&rsquo;s Democratic Republic, Malaysia, Myanmar, Papua New Guinea, Singapore, Thailand, and parts of southeastern China, India, the Solomon Islands, Vanuatu, and Fiji. Twenty-two geographic areas were delineated as tracts that are permissive for porphyry copper deposits in Southeast Asia. Permissive tracts are grouped into four broadly defined geographic/geologic areas, as follows: (1) the Indochina Peninsula area, (2) Indonesian and Malaysian Islands, (3) New Guinea Island and Papuan New Guinea islands, and (4) Melanesia. Individual tracts range from less than 1,000 to more than 350,000 square kilometers in area. Permissive tracts are based on mapped and inferred subsurface (<1 kilometer depth) distributions of igneous rocks of specific age ranges that define magmatic arcs and magmatic belts that are likely to contain porphyry copper deposits. Most of these magmatic arcs are subduction-related, although some have porphyry-style deposits occurring in postcollisional and (or) poorly understood tectonic settings. Although maps at a variety of different scales were used in the compilation, the final tract boundaries are intended for use at a scale of 1:1,000,000. Global grade and tonnage models for porphyry copper deposits were evaluated. Most of the known deposits are best described as fitting the copper-gold (Cu-Au) subtype of porphyry copper deposit. For some permissive tracts, a general porphyry copper-gold-molybdenum (Cu-Au-Mo) model was used. Assessment participants estimated numbers of undiscovered deposits at different levels of confidence for most of the permissive tracts. These estimates were combined with grade and tonnage models using a Monte Carlo simulation to estimate undiscovered resources. Additional resources in extensions of deposits with identified resources were not evaluated. Assessment results, presented in tables and graphs, show mean amounts of metal and mineralized rock in undiscovered deposits at different quantile levels, as well as the arithmetic mean for each tract. This assessment estimated a mean of 89 undiscovered porphyry copper deposits for the assessed permissive tracts in Southeast Asia and Melanesia. About 288 million metric tons (Mt) of copper and 18,000 metric tons (t) of gold, as well as byproduct molybdenum and silver, could be associated with undiscovered deposits. This represents about four times the number of deposits with identified resources (23) already discovered in Southeast Asia; reliable reported identified resources for those 23 deposits total 84 Mt of copper and 6,000 t of gold. Eleven permissive tracts have no known porphyry copper deposits with reported resources. Three of those 11 tracts lacked sufficient information for a probabilistic assessment and are discussed in qualitative terms. On a regional basis, both the Indochina Peninsula area and the Indonesian-Malaysian Islands area are estimated to contain about 10 times as much in place copper in undiscovered porphyry copper deposits as has been identified to date. For the New Guinea Island areas, the ratio of undiscovered to identified copper resources is about 2. Some parts of the region have a long history of porphyry exploration cycles and mine development, interrupted at times by political and social unrest, environmental concerns, and natural disasters. Changes in mining laws within the region and the recent high price of gold on the world market have prompted renewed interest in porphyry copper deposits in Southeast Asia and Melanesia. However, predicted undiscovered deposits may not be found, and if found, may not be developed. This assessment includes an overview of the assessment results with summary tables. Detailed descriptions of each tract are included in appendixes, with estimates of numbers of undiscovered deposits, and probabilistic estimates of amounts of copper, molybdenum, gold, and silver that could be contained in undiscovered deposits for each permissive tract. A geographic information system (GIS) that accompanies the report includes tract boundaries and a database of known porphyry copper deposits and significant prospects.

Scientific Investigations Report↗

The 3D National Topography Model Call for Action—Part 2: The Next Generation 3D Elevation Program

The three-dimensional (3D) National Topography Model initiative to integrate elevation and hydrography data includes the next generation of hydrography data from the 3D Hydrography Program and the next generation of elevation data from the 3D Elevation Program (3DEP). The first-ever collection of light detection and ranging (lidar) data for the nation (IfSAR for Alaska) provides a critical baseline reference, and the addition of multiple repeat elevation mapping projects as part of the next generation of 3DEP would substantially expand analysis capabilities. As the U.S. Geological Survey (USGS) is closing in on our goal of complete coverage with 3DEP data available or in progress for 98.3 percent of the Nation at the end of fiscal year 2024, the USGS is already transitioning to the next generation of 3DEP. Based on the 3D Nation Study results and input from a broad range of stakeholders, the USGS National Geospatial Program has finalized a new design for 3DEP that provides increased lidar quality levels and refresh rates. The new program is designed with more flexibility to meet changing user needs and take advantage of improvements in mapping technologies. The program will aim to expand the level of interagency coordination for topobathymetric lidar acquisition for inland rivers. The next generation of 3DEP will also aim to emphasize research, including advancing program design, products, and services and engaging and leveraging the evolving 3D industry. Research goals also include becoming more flexible in meeting user needs and taking advantage of evolving remote-sensing technologies. The program also plans to move from focusing on producing standard products to producing a concept of a 3D Nation Ecosystem with a variety of inputs, products, and services.

Circular↗

Uplift of the Transantarctic Mountains and the bedrock beneath the East Antarctic ice sheet

In recent years the Transantarctic Mountains (TAM), the largest noncontractional mountain belt in the world, have become the focus of modelers who explained their uplift by a variety of isostatic and thermal mechanisms. A problem with these models is a lack of available data to compare with model predictions. We report here the results of a 312-km-long geophysical traverse conducted in 1993/1994 in the hinterland of the TAM. Using detailed subglacial topography and gravity measurements, we confirm the origin of the TAM as a flexural uplift of the edge of East Antarctica. Using an elastic model with a free edge, we can jointly fit the topography and the gravity with a plate having an elastic thickness of 85±15 km and a preuplift elevation of 700±50 m for East Antarctica. Using a variety of evidence, we argue that the uplift is coincident with a relatively minor tectonic event of transtensional motion between East and West Antarctica during the Eocene rather than the Late Cretaceous rifting event that created the Ross Embayment. We suggest that this transtensional motion caused the continuous plate to break, which created an escarpment that significantly increased the rates of erosion and exhumation. Results from the geophysical traverse also extend our knowledge of the bedrock geology from the exposures within the TAM to the ice covered interior. Our interpretation suggests that the Ferrar flood basalts extend at least 100 km westward under the ice. The Beacon Supergroup of Paleozoic and Mesozoic sediments thins gradually under the ice and its reconstructed thickness is reminiscent of profiles of foreland basins. Finally, there is no indication in the gravity field for an incomplete rebound due to significant melting of the East Antarctic ice sheet since the last glacial period.

Journal of Geophysical Research B: Solid Earth↗

Influence of lamprey rearing type on measures of performance

Declines in populations of Pacific Lamprey (Entosphenus tridentatus) have raised concerns by the Columbia River tribes, who then initiated efforts to protect and restore them throughout their historical range. The Columbia River Inter-Tribal Fish Commission (CRITFC) devised a restoration plan for lamprey in the Columbia River Basin which highlights the significance of lamprey to the tribes and recommends conservation actions. The plan calls for the development of artificial propagation (AP) protocols to provide fish for research (e.g., downstream passage studies) and restoration activities (e.g., supplemental releases into streams/rivers). The ideal outcome of these efforts would be cultured fish that are comparable to the corresponding wild fish, and efforts are underway to conduct such evaluations in larval and juvenile lamprey. The CRITFC lamprey restoration plan lists improving dam passage for juvenile and larval lamprey as a high priority action. Active telemetry techniques have not been an option until recently, when a prototype micro acoustic transmitter was designed for small, elongate fishes like lamprey and eels. Passage survival studies of juvenile and larval lamprey using acoustic telemetry are now possible but are challenged with the limited availability of research animals. The use of AP fish would facilitate passage survival studies, under the assumption that AP juvenile and larval lamprey perform and survive comparably to the wild lamprey they are intended to represent. The current study was enacted to add to the growing knowledge of how reliably AP lamprey can be used as surrogates for wild lamprey. Study objectives were to: 1) compare the swimming ability of AP and wild juvenile lamprey implanted with the prototype micro acoustic transmitter and 2) compare the performance of AP and wild larval lamprey by evaluating night activity levels, burrowing ability, and photokinetic response to tail illumination over a period of 5-months in a culture setting. Evaluations of juvenile lamprey sustained swimming performance did not reveal any differences between tagged and untagged lamprey of AP or wild origin. We standardized the stage of transformation for all tested lamprey to minimize variation. Our tests were constrained by limited access to juvenile lamprey, so significant differences between rearing types may have gone undetected. More information on how rearing type influences other lamprey life stages and swimming performance will add to the growing knowledge on how reliably AP lamprey can serve as surrogates for wild lamprey. We compared AP and wild larval lamprey using three performance metrics, both shortly after they arrived at our laboratory and through a 5-month study period. Within the AP and wild test groups, we divided lamprey into small (30-70 mm total length) and large (80-120 mm total length) size categories, forming four test groups. Each of the test groups were comprised of 25 lamprey and were held in separate tanks. These tanks were the source of test fish for all performance testing. Our results for 2 of 3 of the performance metrics showed no differences between rearing types, and we found limited evidence to suggest that duration in a culture setting changed performance. Night activity levels were low for all test groups. Burrowing times were significantly different by rearing type, with wild lamprey burrowing faster than AP lamprey, in both the small and large size categories. These significant differences in rearing type could be a concern for use of AP lamprey for restoration or research needs, but they may not be biologically meaningful. Both AP and wild lamprey completed burrowing in median times of less than 1 min, which minimizes concerns about predation risk. Additional opportunities to evaluate burrowing performance of AP and wild larval lamprey would be helpful to inform future planned uses of AP lamprey. Finally, our evaluations of photokinetic response to tail illumination revealed similar proportions of AP and wild larvae moving in response to illumination, and no significant differences in response time between the groups. The wild lamprey, however, consistently had faster (but not significantly) response times than AP fish. This finding supports the significantly faster burrowing times we observed for wild lamprey compared to AP fish. Taken together, these lines of evidence raise some concerns for the ability of AP lamprey to serve as defensible surrogates for wild lamprey because the ability to reliably burrow is so critical for larvae. Burrowing performance and photokinetic response to tail illumination were both easy to measure and will be valuable metrics for evaluating rearing types in future studies.

Report↗

Regal fritillary (Speyeria idalia) sex ratio in tallgrass prairie: Effects of survey timing and management regime

The regal fritillary, Speyeria idalia (Drury), was once a common inhabitant of North American grassland communities. Regal fritillary populations are commonly reported to have a male biased adult sex ratio (ASR) throughout their range. We assessed the observed ASR of regal fritillary throughout an annual flight period, investigated how the overall density of both sexes changed, and tested effects of prescribed fire, grazing and haying management treatments on male and female density. We found that regal fritillary exhibited an observed 2:1 male biased ASR across the entire emergence period. Our analysis also revealed that male density peaked earlier than female density in the flight period. Point estimates of density indicated sites that received prescribed burning at the moderate fire-return interval supported ≥1.3 times greater density of males and ≥5.6 times greater density of females versus sites burned with short and long fire-return intervals. Additionally, this effect was enhanced when combined with grazing which showed males were ≥1.9 times and females had ≥1.2 times greater point estimates of density in sites that were grazed and burned at a moderate fire-return interval versus other sites. The relatively stable status of regal fritillary within our study region suggests that a 2:1 male to female ASR may be considered the model composition of populations throughout their range. Likewise, the dynamic nature of the ASR throughout the flight period highlights the importance of conducting surveys across the flight period. Finally, these results corroborate an increasing number of research results that reveal common prairie management practices, such as prescribed fire can be applied within sites that contain regal fritillary and continue to support stable populations.

Kansas↗

Bathymetry and Sediment-Storage Capacity Change in Three Reservoirs on the Lower Susquehanna River, 1996-2008

The Susquehanna River transports a substantial amount of the sediment and nutrient load to the Chesapeake Bay. Upstream of the bay, three large dams and their associated reservoirs trap a large amount of the transported sediment and associated nutrients. During the fall of 2008, the U.S. Geological Survey in cooperation with the Pennsylvania Department of Environmental Protection completed bathymetric surveys of three reservoirs on the lower Susquehanna River to provide an estimate of the remaining sediment-storage capacity. Previous studies indicated the upper two reservoirs were in equilibrium with long-term sediment storage; only the most downstream reservoir retained capacity to trap sediments. A differential global positioning system (DGPS) instrument was used to provide the corresponding coordinate position. Bathymetry data were collected using a single beam 210 kHz (kilohertz) echo sounder at pre-defined transects that matched previous surveys. Final horizontal (X and Y) and vertical (Z) coordinates of the geographic positions and depth to bottom were used to create bathymetric maps of the reservoirs. Results indicated that from 1996 to 2008 about 14,700,000 tons of sediment were deposited in the three reservoirs with the majority (12,000,000 tons) being deposited in Conowingo Reservoir. Approximately 20,000 acre-feet or 30,000,000 tons of remaining storage capacity is available in Conowingo Reservoir. At current transport (3,000,000 tons per year) and deposition (2,000,000 tons per year) rates and with no occurrence of major scour events due to floods, the remaining capacity may be filled in 15 to 20 years. Once the remaining sediment-storage capacity in the reservoirs is filled, sediment and associated phosphorus loads entering the Chesapeake Bay are expected to increase.

Scientific Investigations Report↗

Simulated effects of existing and proposed surface-water impoundments and gas-well pads on streamflow and suspended sediment in the Cypress Creek watershed, Arkansas

Cypress Creek is located in central Arkansas and is the main tributary to Brewer Lake, which serves as the primary water supply for Conway, Arkansas, and the surrounding areas. A model of the Cypress Creek watershed was developed and calibrated in cooperation with Southwestern Energy Company using detailed precipitation, streamflow, and discrete suspended-sediment data collected from 2009 through 2012. These data were used with a Hydrologic Simulation Program&mdash;FORTRAN model to address different potential gas-extraction activities within the watershed. The calibrated Hydrologic Simulation Program&mdash;FORTRAN model was used to simulate four land-use scenarios and examine the potential effects of these land-use changes on the streamflow and water quality within the Cypress Creek watershed. These simulated scenarios included (1) the conversion of all nonforested land to forest, representing a time period before extensive grazing activities and no gas-extraction activities; (2) a land-use change to that of 1949, representing a time period with some grazing activities and no gas-extraction activities; (3) a time period with current land-use conditions, but without any gas-extraction activities, that is, the exclusion of gas-well pads/pipelines, associated gravel roads, and surface-water impoundments; and (4) a time period with current land-use conditions, but with increased gas-extraction activities (for example, increased gas-well pad and surface-water impoundment activities) to represent a possible future natural gas full-development condition for the area. A current-conditions simulation also was built and calibrated and represents the current conditions (2013) within the watershed. This simulation was used as the comparison basis for the four land-use scenarios described above. The current-conditions simulation used the 2006 land-use conditions, which consisted primarily of forest and pasture, as well as the current (2013) 35 gas-well pads and pipelines and 6 surface-water impoundments, which account for approximately 1.6 percent of the land use. Simulating a time period before extensive-grazing activities and no gas-extraction activities for scenario 1 resulted in a decrease in suspended-sediment loads and volume of streamflow within the Cypress Creek watershed compared to the current-conditions simulation. Simulating a time period before any gas-extraction activities but with some grazing activities for scenario 2 also resulted in a decrease in suspended-sediment loads and volume of streamflow within the Cypress Creek watershed. Simulating current conditions, but without any natural gas-pad land use or related activities (including pipelines and associated gravel roads), for scenario 3 resulted in mostly unchanged suspended-sediment loads and volume of streamflow within the Cypress Creek watershed, as compared to the current-conditions simulation. Finally, simulating potential future conditions of increased gas-well pad and surface-water impoundment activities for scenario 4 resulted in a decrease (compared to the current-conditions simulation) in suspended-sediment loads and a slight increase of volume of streamflow within the Cypress Creek watershed. The Arkansas Natural Resources Commission and the Arkansas Department of Environmental Quality list suspended sediment from &ldquo;poor pastures&rdquo; as a primary source of nonpoint-source pollution in north-central Arkansas, but unpaved (gravel) roads are another important source of suspended sediment. Because of the high sediment-loading rates associated with gravel roads and the large amount of pasture within the watershed, the factors most responsible for suspended sediment within the Cypress Creek watershed are likely associated more with the pastureland and gravel roads, than factors associated with gas-well pads/pipelines.

Arkansas↗

Monitoring the recovery of seabirds and forage fish following a major ecosystem disruption in Lower Cook Inlet

Following the North Pacific marine heatwave of 2014-2016 and associated extreme die-off of seabirds in the winter of 2015-2016, we repeated historical marine bird and forage fish surveys around two seabird colonies (Gull Island, Chisik Island) in lower Cook Inlet during 2016-2019 in order to document immediate and lingering impacts of the heatwave on resident fish and seabird populations. At sea, we conducted acoustic/trawl surveys for fish in near-colony areas, while simultaneously counting seabirds on survey transects. At colonies, we monitored bird numbers on whole colony censuses and population plot counts and assessed annual reproductive success of Black-legged Kittiwakes ( Rissa tridactyla ) and Common Murres ( Uria aalge ). Our studies suggest that impacts of the heatwave on seabirds and their forage base were severe and extended for several years beyond the heatwave itself. Although fish biomass indices were greatest in 2016-2017, the forage community was largely dominated by juvenile fish with low nutritional value following a collapse of key species of forage fish during the marine heatwave. Lowest fish biomass was observed in 2018, coincident with a marked decline in the at-sea abundance of many seabirds around colonies. By 2019 there were signs of improvement in prey abundance and quality, and significant aggregations of pre-spawning capelin and large sand lance were observed in and around Kachemak Bay. In comparison with historical (1996-1999) bird colony surveys, kittiwake population counts decreased by more than 70% at Chisik Island, and by 8-29% at Gull Island. Similarly, murre counts decreased at Chisik Island by 72% and by more than 20% at Gull Island. Kittiwakes had complete reproductive failure at Chisik Island from 2016-2018, with minimal success in 2019. At Gull Island, kittiwakes also failed in 2016 and 2018 but had unusually high productivity in 2017 and 2019. Murres also had complete reproductive failures at Chisik Island in all four years and at Gull Island during 2016, 2017 and 2018. Murres finally fledged chicks in 2019, albeit at about half the normal rate. Finally, we also observed unusually high levels of predator disturbance (egg predation, flushing adults from plots) and unprecedented numbers of adult birds in poor body condition (“skinny murres”), particularly in 2018. Together, these results indicate that an extreme disruption of marine food webs occurred during and after the heatwave. Given the prolonged reproductive failures, continued monitoring is required to assess continuing impacts and recovery from the 2014-2016 heatwave. For example, murre chicks that would have been produced in 2016 should, after 4-5 years away, start recruiting to the colony in 2021, and thereby replace aged adults that would have died naturally in the past year(s). Without such natal recruitment for at least the next 3-4 years, we should document a continuing decline in bird numbers at the colonies.

Alaska↗

Research to improve ShakeAlert earthquake early warning products and their utility

Earthquake early warning (EEW) is the rapid detection of an earthquake and issuance of an alert or notification to people and vulnerable systems likely to experience potentially damaging ground shaking. The level of ground shaking that is considered damaging is defined by the specific application; for example, manufacturing equipment may experience damage at a lower intensity ground shaking than would cause damage to a building. Along the West Coast of the United States, the warning times for ground shaking could range as high as tens of seconds for moderate levels of ground shaking, or potentially longer, if a lower ground-shaking threshold is used to issue alerts. However, it is not always possible to provide advance warning of ground shaking, particularly for locations close to an earthquake that are most likely to experience very strong ground shaking. EEW alerts may be useful to individuals who can use a few seconds to move to a safe zone and to electromechanical systems that can take automatic actions to reduce damage and injuries. An EEW system, ShakeAlert, has been under development in the United States since 2006. Federal and State governments, as well as the private sector, are now investing in the ShakeAlert prototype system that will, when completed, become an operational public system for the West Coast of the United States. While the current prototype is delivering alerts to test users, improvements to the accuracy, timeliness, and utility of the alerts are needed. For this reason, it is essential that the ShakeAlert system be continuously improved through targeted research, involving not only the current ShakeAlert partner organizations, but also the broader scientific, engineering, and emergencyresponse communities. To this end, this report describes the opportunities for improvement that can be addressed through research and development over the next 5 years. Our recommendations are organized into four areas: (1) understand EEW capabilities and user needs, (2) make alerts as fast and accurate as possible, (3) ensure reliability when it counts, and (4) explore the use of new instrumentation. The first challenge is to understand EEW capabilities and user needs. EEW must deliver actionable information to people and to automated systems to mitigate short- and longterm impacts of damaging ground shaking, so development of EEW must be motivated by the needs of users. Within this challenge, we must study the technical capabilities and limitations of EEW in general, and the ShakeAlert system specifically. This includes development of performance metrics that assess the timeliness and accuracy of alerts to understand the value and utility of the ShakeAlert EEW product(s) for various user groups, including different industry sectors, emergency-management agencies, and the public. Research is needed to define the alerting choices that maximize the utility of the system for users and to determine what the available communication pathways are for providing timely alert information. Additionally, we engage users to assess how alerts will be used by different sectors to mitigate losses and to inform EEW product design. Further, social-science research is needed to develop alert messaging, including what relevant prior and follow-up information are required, to ensure effective use of alerts. The second challenge is to make alerts as fast and as accurate as possible. The timeliness and accuracy of an EEW alert is important because it will set in motion a series of actions and downstream products. An EEW alert will trigger notification across emergency-alert systems and across multiple communication channels to populations in impacted regions. The EEW alert region may grow as the earthquake fault-rupture length increases, and the EEW system’s characterization of it, evolves. We must continue research into new or improved seismic and geodetic waveform-processing methods necessary to rapidly characterize the expected ground shaking and associated uncertainties. It is important to thoroughly evaluate whether new methods improve alerts through more accurate ground-motion estimates and (or) reduced latencies (that is, longer warning times). New methods could include tracking the extent of a large rupture in real time (known as finite-fault algorithms) and ground-motionbased EEW algorithms. Additionally, ground motion predictions could be optimized for each earthquake as the earthquake fault rupture progresses by using, for example, event terms to shift ground-motion curves for more (or less) energetic ruptures. The third challenge is to ensure reliability when it counts. This challenge requires us to explore approaches that assess the expected performance of ShakeAlert across the range of earthquake magnitudes, locations, and depths that may occur within the alerting region. Large, damaging earthquakes and their associated aftershock sequences matter most for hazard and for EEW, but these large-earthquake sequences occur infrequently. We expect ShakeAlert to respond robustly to these large-earthquake sequences despite potentially long periods of relative seismic quiescence in the intervening years, and in spite of inevitable communication challenges that arise during and after a large earthquake. We must develop methods to utilize the broadest available datasets to test EEW performance, including ground-motion data recorded in other parts of the world. The observational period for large, damaging earthquakes in any particular region has been short in comparison to estimated large-earthquake recurrence times. Ground-motion records for very large, damaging western United States events and major aftershock sequences do not yet exist, nor do data exist for all potential sources of noise and spurious signals that ShakeAlert must be “tuned” to reject. In addition, robust synthetic data could provide the flexibility to test a wider range of earthquake magnitude, tectonic-setting, and noise scenarios than are covered by existing observational data. Synthetic ground-motion data must be thoroughly vetted against records of smaller magnitude earthquakes to ensure that they accurately capture both the onset and the amplitude of the ground shaking. The final challenge is to explore the use of new instrumentation. The development of EEW around the world to date has focused on the use of high-quality, scientific-grade seismic and geodetic instrumentation. The use of additional types of instrumentation or information may also improve EEW products by filling gaps in sensor coverage in countries that already have dense seismic networks or enable EEW in countries without such networks. We must keep up with these developments and continuously assess their value in supplementing existing EEW systems, such as ShakeAlert, or enabling EEW where such systems do not exist. Such developments include low-cost instrumentation with microelectromechanical system (MEMS) sensors and global positioning system (GPS)/global navigation satellite system (GNSS) antennas embedded in low-cost consumer electronics, sea-floor seismometers, geodetic instrumentation deployed along the Cascadia and Alaska megathrust margins of western North America, and borehole strainmeters that are already deployed across the region.

Open-File Report↗

2007 Rocky Mountain section Friends of the Pleistocene field trip - Quaternary geology of the San Luis basin of Colorado and New Mexico, September 7-9, 2007

Prologue Welcome to the 2007 Rocky Mountain Cell Friends of the Pleistocene Field Trip, which will concentrate on the Quaternary geology of the San Luis Basin of Colorado and New Mexico. To our best knowledge, Friends of the Pleistocene (FOP) has never run a trip through the San Luis Basin, although former trips in the region reviewed the 'Northern Rio Grande rift' in 1987 and the 'Landscape History and Processes on the Pajarito Plateau' in 1996. After nearly a decade, the FOP has returned to the Rio Grande rift, but to an area that has rarely hosted a trip with a Quaternary focus. The objective of FOP trips is to review - in the field - new and exciting research on Quaternary geoscience, typically research being conducted by graduate students. In our case, the research is more topically oriented around three areas of the San Luis Basin, and it is being conducted by a wide range of Federal, State, academic, and consulting geologists. This year's trip is ambitious?we will spend our first day mainly on the Holocene record around Great Sand Dunes National Park and Preserve, the second day on the Quaternary stratigraphy around the San Luis Hills, including evidence for Lake Alamosa and the 1.0 Ma Mesita volcano, and wrap up the trip's third day in the Costilla Plain and Sunshine Valley reviewing alluvial stratigraphy, the history of the Rio Grande, and evidence for young movement on the Sangre de Cristo fault zone. In the tradition of FOP trips, we will be camping along the field trip route for this meeting. On the night before our trip, we will be at the Great Sand Dunes National Park and Preserve's Pinyon Flats Campground, a group facility located about 2 miles north of the Visitors Center. After the first day's trip, we will dine and camp in the Bachus pit, about 3 miles southwest of Alamosa. For the final night (after day 2), we will bed down at La Junta Campground at the Bureau of Land Management (BLM) Wild and Scenic Rivers State Recreation Area, west of Questa, New Mexico, overlooking a majestic canyons of the Rio Grande and Red River. This is the 48th meeting of the Rocky Mountain Section of FOP, which was initiated by Gerry Richmond (USGS-Denver, deceased) in 1952 (see the following table, which lists all the Rocky Mountain Section field trips). The Rocky Mountain Section has been inactive for three years owing to a series of problems, including an unfortunate cancellation of Dennis Dahms' trip to the southern Wind River Range in 2005. Hopefully, this year's trip will provide the logistical initiative and scientific momentum for future Friends of the Pleistocene trips in the Rocky Mountain region.

Colorado, New Mexico↗

Final Project Memorandum: Ecological implications of mangrove forest migration in the southeastern U.S.

Winter climate change has the potential to have a large impact on coastal wetlands in the southeastern United States. Warmer winter temperatures and reductions in the intensity of freeze events would likely lead to mangrove forest range expansion and salt marsh displacement in parts of the U.S. Gulf of Mexico and Atlantic coast. The objective of this research was to better evaluate the ecological implications of mangrove forest migration and salt marsh displacement. The potential ecological impacts of mangrove migration are diverse ranging from important biotic impacts (e.g., coastal fisheries, land bird migration; colonial-nesting wading birds) to ecosystem stability (e.g., response to sea level rise and drought; habitat loss; coastal protection) to biogeochemical processes (e.g., carbon storage; water quality). This research specifically investigated the impact of mangrove forest migration on coastal wetland soil processes and the consequent implications for coastal wetland responses to sea level rise and carbon storage.

Report↗

Simulation of ground-water flow in the High Plains aquifer, southern sandhills area, west-central Nebraska

A generalized ground-water flow model was prepared for the High Plains aquifer in the southern sandhills area of west-central Nebraska. A grid of 4- by 4-mile nodes was established over the study area. Steady-state water levels were simulated using a distribution of recharge from a soil-moisture budget model and from estimates of hydraulic conductivity obtained from logs of test holes in the area. The final calibrated simulation used hydraulic- conductivity values that were 122 percent, and recharge rates that were 89 percent of the original values used in the model. Sixty-seven percent of the simulated recharge to the High Plains aquifer discharges to rivers, streams, and lakes. Discharges through ground-water evapotranspiration and from pumping wells account for 20 percent, with the wells accounting for less than 10 percent of the total discharge, and subsurface boundary outflow accounts for 13 percent. Twenty years of simulated pumping, assuming one additional well would be added to each township annually for 10 years, and two wells per township would be added each year for the succeeding 10 years, produced a maximum simulated drawdown of less than 10 feet when a uniform specific yield of 16 percent for the aquifer in the study area was assumed.

Open-File Report↗

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↗

Completion Summary for Well NRF-16 near the Naval Reactors Facility, Idaho National Laboratory, Idaho

In 2009, the U.S. Geological Survey in cooperation with the U.S. Department of Energy's Naval Reactors Laboratory Field Office, Idaho Branch Office cored and completed well NRF-16 for monitoring the eastern Snake River Plain (SRP) aquifer. The borehole was initially cored to a depth of 425 feet below land surface and water samples and geophysical data were collected and analyzed to determine if well NRF-16 would meet criteria requested by Naval Reactors Facility (NRF) for a new upgradient well. Final construction continued after initial water samples and geophysical data indicated that NRF-16 would produce chemical concentrations representative of upgradient aquifer water not influenced by NRF facility disposal, and that the well was capable of producing sustainable discharge for ongoing monitoring. The borehole was reamed and constructed as a Comprehensive Environmental Response Compensation and Liability Act monitoring well complete with screen and dedicated pump. Geophysical and borehole video logs were collected after coring and final completion of the monitoring well. Geophysical logs were examined in conjunction with the borehole core to identify primary flow paths for groundwater, which are believed to occur in the intervals of fractured and vesicular basalt and to describe borehole lithology in detail. Geophysical data also were examined to look for evidence of perched water and the extent of the annular seal after cement grouting the casing in place. Borehole videos were collected to confirm that no perched water was present and to examine the borehole before and after setting the screen in well NRF-16. Two consecutive single-well aquifer tests to define hydraulic characteristics for well NRF-16 were conducted in the eastern SRP aquifer. Transmissivity and hydraulic conductivity averaged from the aquifer tests were 4.8 x 103 ft2/d and 9.9 ft/d, respectively. The transmissivity for well NRF-16 was within the range of values determined from past aquifer tests in other wells near NRF of 4.4 x 102 to 5.1 x 105 ft2/d. Water samples were analyzed for metals, nutrients, total organic carbon, volatile organic compounds, semi-volatile organic compounds, herbicides, pesticides, polychlorinated biphenols, and radionuclides. All chloride, nitrate, and sulfate concentrations were less than background concentrations for the eastern SRP aquifer north of the NRF. Concentrations in water samples for most of the organic compounds and radionuclides were less than the reporting limits and reporting levels.

Scientific Investigations Report↗

Parameter estimation method and updating of regional prediction equations for ungaged sites in the desert region of California

The U.S. Geological Survey (USGS) is currently updating at-site flood frequency estimates for USGS streamflow-gaging stations in the desert region of California. The at-site flood-frequency analysis is complicated by short record lengths (less than 20 years is common) and numerous zero flows/low outliers at many sites. Estimates of the three parameters (mean, standard deviation, and skew) required for fitting the log Pearson Type 3 (LP3) distribution are likely to be highly unreliable based on the limited and heavily censored at-site data. In a generalization of the recommendations in Bulletin 17B, a regional analysis was used to develop regional estimates of all three parameters (mean, standard deviation, and skew) of the LP3 distribution. A regional skew value of zero from a previously published report was used with a new estimated mean squared error (MSE) of 0.20. A weighted least squares (WLS) regression method was used to develop both a regional standard deviation and a mean model based on annual peak-discharge data for 33 USGS stations throughout California&rsquo;s desert region. At-site standard deviation and mean values were determined by using an expected moments algorithm (EMA) method for fitting the LP3 distribution to the logarithms of annual peak-discharge data. Additionally, a multiple Grubbs-Beck (MGB) test, a generalization of the test recommended in Bulletin 17B, was used for detecting multiple potentially influential low outliers in a flood series. The WLS regression found that no basin characteristics could explain the variability of standard deviation. Consequently, a constant regional standard deviation model was selected, resulting in a log-space value of 0.91 with a MSE of 0.03 log units. Yet drainage area was found to be statistically significant at explaining the site-to-site variability in mean. The linear WLS regional mean model based on drainage area had a Pseudo- 2 R of 51 percent and a MSE of 0.32 log units. The regional parameter estimates were then used to develop a set of equations for estimating flows with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities for ungaged basins. The final equations are functions of drainage area.Average standard errors of prediction for these regression equations range from 214.2 to 856.2 percent.

California↗

Spatial and temporal variation of stream chemistry associated with contrasting geology and land-use patterns in the Chesapeake Bay watershed—Summary of results from Smith Creek, Virginia; Upper Chester River, Maryland; Conewago Creek, Pennsylvania; and Difficult Run, Virginia, 2010–2013

Despite widespread and ongoing implementation of conservation practices throughout the Chesapeake Bay watershed, water quality continues to be degraded by excess sediment and nutrient inputs. While the Chesapeake Bay Program has developed and maintains a large-scale and long-term monitoring network to detect improvements in water quality throughout the watershed, fewer resources have been allocated for monitoring smaller watersheds, even though water-quality improvements that may result from the implementation of conservation practices are likely to be first detected at smaller watershed scales. In 2010, the U.S. Geological Survey partnered with the U.S. Environmental Protection Agency and the U.S. Department of Agriculture to initiate water-quality monitoring in four selected small watersheds that were targeted for increased implementation of conservation practices. Smith Creek watershed is an agricultural watershed in the Shenandoah Valley of Virginia that is dominated by cattle and poultry production, and the Upper Chester River watershed is an agricultural watershed on the Eastern Shore of Maryland that is dominated by row-cropping activities. The Conewago Creek watershed is an agricultural watershed in southeastern Pennsylvania that is characterized by mixed agricultural activities. The fourth watershed, Difficult Run, is a suburban watershed in northern Virginia that is dominated by medium density residential development. The objective of this study was to investigate spatial and temporal variations in water chemistry and suspended sediment in these four relatively small watersheds that represent a range of land-use patterns and underlying geology to (1) characterize current water-quality conditions in these watersheds, and (2) identify the dominant sources, sinks, and transport processes in each watershed. The general study design involved two components. The first included intensive routine water-quality monitoring at an existing streamgage within each study area (including continuous water-quality monitoring as well as discrete water-quality sampling) to develop a detailed understanding of the temporal and hydrologic variability in stream chemistry and sediment transport in each watershed. The second component involved extensive water-quality monitoring at various sites throughout each watershed to develop a detailed understanding of spatial patterns. Both components were used to improve understanding of sources and transport processes affecting stream chemistry, including nutrients and suspended sediments, and their implications for detecting long-term trends related to best management practices. This report summarizes the results of monitoring that was performed from April 2010 through September 2013. Individual Small Watershed Summaries Summaries for each of the four small watersheds are presented below. Each watershed has a more descriptive and detailed section in the report, but these summaries may be particularly useful for some watershed managers and stakeholders desiring slightly less technical detail. Smith Creek Smith Creek is a 105.39-mi 2 watershed within the Shenandoah Valley that drains to the North Fork Shenandoah River. The long-term Smith Creek base-flow index is 72.3 percent, indicating that on average, approximately 72 percent of Smith Creek flow was base flow, which suggests that Smith Creek streamflow is dominated by groundwater discharge rather than stormwater runoff. A series of cluster and principal components analyses demonstrated that the majority of the variability in Smith Creek water quality could be attributed to hydrologic and seasonal variability. Statistically significant positive correlations with flow were observed for turbidity, suspended sediments, total nitrogen, ammonium, orthophosphate, iron, total phosphorus, and the ratio of calcium to magnesium. Statistically significant inverse correlations with flow were observed for specific conductance, magnesium, δ 15 N of nitrate, pH, bicarbonate, calcium, and δ 18 O of nitrate. Of particular note, flow and nitrate were not statistically significantly correlated, likely because of the relatively complex concentration-discharge relationship observed in continuous and discrete datasets. Statistically significant seasonal patterns were observed for numerous water-quality constituents: water temperature, turbidity, orthophosphate, total phosphorus, suspended-sediment concentration, and silica were higher during the warm season, but pH, dissolved oxygen, and sulfate were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient loads in Smith Creek using the continuous water-quality monitors. The mean Smith Creek in-stream sediment load was approximately 6,900 tons per year, with nearly 90 percent of the sediment load over the 3-year study period contributed during the eight largest storm events during that period. The Smith Creek total phosphorus load was approximately 21,000 pounds of phosphorus per year, with the majority of the load contributed during stormflow periods, although a substantial phosphorus load still occurs during base-flow conditions. The Smith Creek total nitrogen load was approximately 400,000 pounds per year, with total nitrogen accumulation less dominated by stormflow contributions (as was the case for sediment and total phosphorus) and strongly affected by base-flow export of nitrogen from the basin. Extensive water-quality monitoring throughout the Smith Creek watershed revealed how the complex geology and hydrology interacted to result in variable water chemistry. During relatively dry and low base-flow periods, much of the discharge in Smith Creek was contributed by a single dominant spring—Lacey Spring. During wetter base-flow periods, the flows in Smith Creek were largely generated by a mixture of headwater springs and forested mountain tributaries with very different geochemical composition. The headwater springs generally issued from limestone bedrock and were characterized as having relatively high nitrate, specific conductance, calcium, and magnesium, as well as relatively low concentrations of phosphorus, ammonium, iron, and manganese. The undeveloped, high-gradient, forested mountain sites were generally characterized by low ionic strength waters with low nutrient concentrations. Nitrate isotope data from the limestone springs generally were consistent with manure-derived nitrogen sources (such as cattle and poultry), although the possibility of other mixed sources cannot be excluded. Nitrate isotope data from the undeveloped, high-gradient forested mountain sites were more consistent with nitrogen from undisturbed soils, atmospheric deposition, or nitrogen fixation. Regardless of the nitrogen source, oxygen isotope data indicate that the nitrate was largely a result of nitrification. Land-use data indicate that manure sources of nitrogen dominated watershed nitrogen inputs. Phosphorus sources were less well studied. The presence of a single point-source discharge near the town of New Market contributed the majority of the phosphorus to Smith Creek under base-flow conditions, but nonpoint sources of phosphorus dominated the loading to Smith Creek during stormflow periods. Implementation of conservation practices increased in the Smith Creek watershed during the study period, and even though a broad range of practice types was implemented, the most common practices included stream fencing (for cattle exclusion), the development of nutrient management plans, conservation crop rotation, and the planting of cover crops. While the implementation of these conservation practices is encouraging, results indicate small increases in nitrate concentrations at the streamgage over the last 29 years, concurrent with small decreases in nitrate fluxes. It will likely be years before the cumulative effect of these practices can be detected in the Smith Creek water quality, and the magnitude of the effect of these conservation practices detected in Smith Creek will depend largely on whether nutrient loading (of manure and commercial fertilizer) is reduced over time. Upper Chester River The Upper Chester River watershed includes the 36-square-mile (mi 2 ) watershed area around several nontidal tributaries that drain into the tidal Chester River. The streamgage is on Chesterville Branch, the largest nontidal tributary (approximately 6.12 mi 2 ) and is the site for continuous water-quality monitoring for this project. The base-flow index at Chesterville Branch is about 72 percent and indicates that, as in most of the Coastal Plain, groundwater is the greatest contributor to streamflow. As such, more than 90 percent of the nitrogen in the stream is in the form of nitrate from groundwater. Continuous and discrete data collected at Chesterville Branch show the effects of streamflow and season on water quality. Significantly positive correlations with flow were observed for ammonium, dissolved and total phosphorus, sediment, and turbidity as runoff carried these constituents from the land surface into Chesterville Branch. Other constituents that increased significantly with flow include potassium, sulfate, iron, and manganese, which are likely contributed from near-stream areas and ponds with high organic-matter content. Total nitrogen, pH, and specific conductance, along with chemical constituents associated with groundwater inputs including nitrate, calcium, ratio of calcium to magnesium, silica, bicarbonate, and sodium, were negatively correlated with flow because concentrations of these constituents were diluted by runoff. Seasonal differences in water chemistry, which are most likely related to increased biologic effects on the uptake and release of chemicals in the stream and near-stream areas, also were observed. Water temperature, orthophosphate, δ 15 N of nitrate, bicarbonate, sodium, and the ratio of sodium to chloride were higher during the warm season, and dissolved oxygen, total nitrogen, nitrate, magnesium, sulfate, and manganese were higher during the cool season. Surrogate-regression models developed by using continuous water-quality data showed that the annual sediment load for the 2013 water year was about 2,600 tons, with more than 90 percent of this sediment contributed during two storms. The total phosphorus load in 2013 was about 13,000 pounds with more than 90 percent contributed during the same two storms as sediment. The load of total nitrogen, 140,000 pounds, accumulated steadily throughout the 2013 water year as nitrate in groundwater continuously discharged into the stream. The same two large storms that contributed 90 percent of the suspended-sediment and total phosphorus load only contributed about 20 percent of the annual total nitrogen load. Extensive water-quality monitoring of stream base flow throughout the Upper Chester River watershed identified how differences in land use and hydrogeology affected water chemistry. In parts of the watershed with well-drained soil and thick sandy aquifer sediments, concentrations of nitrate and other chemicals associated with fertilizer and lime application increased in streams as agricultural land use increased. More than 90 percent of the nitrogen in streams from these areas was in the form of nitrate, and concentrations ranged from about 5 milligrams per liter (mg/L) to 8 mg/L as nitrogen in the two largest tributaries. Stream nitrate concentrations were about 1 mg/L as nitrogen where soils were more poorly drained, the surficial aquifer sediments were thinner, and forests and wetlands were more widespread than agriculture. Nitrate isotope data were consistent with inorganic fertilizers ± atmospheric deposition and N 2 fixation as sources of nitrogen, and with nitrification as the dominant nitrate-forming process. Nitrate reduction was indicated by elevated δ 15 N and δ 18 O values in some samples from streams draining watersheds with poorly drained soils. An analysis of land-use data and SPARROW modeling input data attributed almost 90 percent of the nitrogen sources in the Upper Chester River watershed to inorganic fertilizer and fixation of atmospheric nitrogen by legumes, which is in agreement with the isotopic characteristics of nitrate in this watershed. Local sources of manure are limited in this area. Total phosphorus concentrations during base flow ranged from below detection to about 0.2 mg/L. Stream phosphorus concentrations during base flow were generally lower than those measured during storms because most phosphorus transport likely occurs as phosphorus attached to sediment particles during runoff. Because manure is not widely used in this area, the major source of phosphorus is likely fertilizer. The implementation of conservation practices in the Upper Chester River watershed increased substantially during the study period, with a total implementation of 1,194 U.S. Department of Agriculture-compliant practices. The most frequently used practices were oriented towards nutrient and sediment control, including cover crops, nutrient management planning, conservation crop rotation, conservation tillage, and irrigation management. The current Chesapeake Bay model for this area predicts that implementation of best management practices should result in a 13-percent decrease in overall delivery of nitrogen to the Upper Chester River. Because most nitrogen travels through the groundwater system for years to decades before being discharged to streams, the time period of monitoring was not sufficient to see the effects of these practices on water quality. The magnitude of the effect that may eventually be detected will depend on the degree to which nitrate leaching into the groundwater system is reduced over time. Loadings of phosphorus and sediment are primarily transported during large runoff events and are difficult to control and analyze for trends because of their timing and episodic nature. Conewago Creek Conewago Creek has two primary monitoring locations—one near the middle of the 47-mi 2 watershed and the other near the outlet just upstream of the Susquehanna River. The base-flow index was 47.3 percent for 2012–2013, indicating that on average, approximately 53 percent of the streamflow in Conewago Creek exited the watershed as surface flow, which suggests that the stormwater runoff was somewhat greater than groundwater discharge (base flow). A series of cluster and principal components analyses demonstrated that the majority of the variability in the Conewago Creek water quality could be attributed to hydrologic and seasonal variability. Statistically significant positive correlations with flow were observed at both monitoring sites for ammonium, total phosphorus, orthophosphate, iron, and manganese; additionally, at the upstream monitoring station, total nitrogen demonstrated a statistically significant positive correlation with flow. Statistically significant inverse correlations with flow were observed at both sites for water temperature, specific conductance (at the downstream site only), sulfate, chloride, calcium, and magnesium. Statistically significant seasonal patterns were observed for several water-quality constituents. Water temperature, phosphorus (upstream site only), and orthophosphate were higher during the warm season, and nitrate and total nitrogen (upstream site only) were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient load in Conewago Creek by using the continuous water-quality monitors and water-quality samples. Conewago Creek sediment load was approximately 9,900 tons in 2012 and approximately 18,900 tons in 2013, with nearly 80 percent of the sediment load in 2013 contributed by the three largest storm events. Annual total nitrogen loads could not be estimated due to poor model performance. The addition of continued monitoring or a continuously recording nitrate sensor could improve estimates of total nitrogen loads. During 2012 and 2013, phosphorus loads in Conewago Creek were approximately 50,000 pounds in each year. Combining data from one high-flow synoptic sampling with the data from routine sampling revealed how the geology and hydrology interact to result in variable water chemistry throughout the Conewago Creek watershed. The areas above the upstream gage in the headwaters are generally underlain by forested non-carbonate bedrock and are characterized by relatively low nitrate, specific conductance, calcium, and magnesium, as well as relatively low concentrations of phosphorus, ammonium, iron, and manganese. The more developed, agricultural areas below the upstream site were generally characterized by higher ionic strength waters with higher nutrient and metal concentrations. An analysis of land-use data and SPAtially Referenced Regressions On Watershed (SPARROW) modeling data indicates that manure sources of nitrogen dominate the input of nitrogen to the watershed. Implementation of conservation practices increased in the Conewago Creek watershed during the study period, and while a broad range of practice types were implemented, the most common practices included residue and tillage management, cover crops, nutrient management, terracing, and stream fencing (for animal exclusion or bank restoration). While the implementation of these conservation practices is encouraging, the cumulative effects of these practices probably will not be detected in Conewago Creek water quality for several years. The magnitude of the effects of these conservation practices on water quality in Conewago Creek will depend largely on the extent to which nutrient loading (septic, manure, and commercial fertilizer) and sediment-producing activities are reduced over time. Difficult Run The Difficult Run watershed is a 57.82-mi 2 watershed that drains to the Potomac River. The long-term Difficult Run base-flow index (from 1936 to 2010) was 57.9, indicating that approximately 58 percent of streamflow exited the watershed as base flow and 42 percent as stormflow; however, with continued development and urbanization of the watershed, the base-flow index has decreased to 50 percent during the last 20 years. This base-flow index was less than those of the other watersheds evaluated in this study, likely because the Difficult Run watershed largely is underlain by crystalline piedmont metamorphic rocks and has a greater proportion of impervious urban land cover. A series of cluster and principal components analyses indicated that most of the variability in Difficult Run water quality could be attributed to hydrologic variability and seasonality. Statistically significant positive correlations with flow were observed for turbidity, dissolved oxygen, suspended sediments, ammonium, orthophosphate, iron, and total phosphorus. Statistically significant inverse correlations with flow were observed for water temperature, pH, specific conductance, bicarbonate, calcium, magnesium, nitrate, δ 15 N of nitrate, and silica. Statistically significant seasonal patterns were observed for numerous water-quality constituents: water temperature, ammonium, orthophosphate, and δ 15 N of nitrate were higher during the warm season, and dissolved oxygen, nitrate, and manganese were higher during the cool season. Surrogate regression models were developed to compute sediment and nutrient loading rates. The Difficult Run sediment load was approximately 8,000 tons per year, with greater than 95 percent of the sediment load in the 2013 water year contributed by the seven largest storm events. The total phosphorus load in Difficult Run was approximately 14,000 pounds of phosphorus per year, with the majority of the load contributed during stormflow periods. The total nitrogen load in Difficult Run is estimated to have been approximately 140,000 pounds per year, with total nitrogen accumulation less dominated by stormflow contributions than that of phosphorus and strongly affected by base-flow export of nitrogen from the basin. Extensive water-quality monitoring throughout the Difficult Run watershed revealed relatively uniform generation of flow per unit of watershed area, as well as spatial variation in water quality that is strongly related to land-use activities. Elevated nitrate concentrations were observed in a subset of monitoring sites that are inversely correlated with population density and positively correlated to the septic system density within each subwatershed. The majority of the elevated nitrate concentrations for these sites are hypothesized to be caused by nitrate leaching from septic systems, more so than homeowner fertilizer usage among these subwatersheds that have lower population densities than other parts of the watershed. Nitrate isotope data, temporal patterns in the water-quality data, mass-balance computations, and a separate land-use analysis all generally indicate that leachate from septic systems was the likely source of the elevated nitrate. Another group of water-quality sites have relatively low nitrogen concentrations, are located in areas that are served by city sewer lines, and have experienced stream restoration activities. A final group of sites drained the areas with the highest imperviousness and had strongly elevated specific conductance, chloride, and sodium, which were likely caused by a combination of road salting and other anthropogenic sources draining these urbanized areas in the watershed. A fourth group of sites represents a mixture of water sources and had water quality similar to that at the Difficult Run streamgage. Analysis of the nitrate isotope data generally indicates a broad range of composition indicative of mixed natural and anthropogenic nitrogen sources. Implementation of conservation practices increased in the Difficult Run watershed during the study period, and while a broad range of practice types was implemented, the most common practices included stream restoration. While the implementation of these conservation practices is encouraging, the cumulative effect of these practices probably will not be detected in Difficult Run water quality for several years.

Maryland, Pennsylvania, Virginia↗