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USGS2007

Geosoft eXecutables (GX's) Developed by the U.S. Geological Survey, Version 2.0, with Notes on GX Development from Fortran Code

Introduction Geosoft executables (GX's) are custom software modules for use with the Geosoft Oasis montaj geophysical data processing system, which currently runs under the Microsoft Windows 2000 or XP operating systems. The U.S. Geological Survey (USGS) uses Oasis montaj primarily for the processing and display of airborne geophysical data. The ability to add custom software modules to the Oasis montaj system is a feature employed by the USGS in order to take advantage of the large number of geophysical algorithms developed by the USGS during the past half century. This main part of this report, along with Appendix 1, describes Version 2.0 GX's developed by the USGS or specifically for the USGS by contractors. These GX's perform both basic and advanced operations. Version 1.0 GX's developed by the USGS were described by Phillips and others (2003), and are included in Version 2.0. Appendix 1 contains the help files for the individual GX's. Appendix 2 describes the new method that was used to create the compiled GX files, starting from legacy Fortran source code. Although the new method shares many steps with the approach presented in the Geosoft GX Developer manual, it differs from that approach in that it uses free, open-source Fortran and C compilers and avoids all Fortran-to-C conversion.

Open-File Report↗

USGS2007

Climate variation at Flagstaff, Arizona - 1950 to 2007

Much scientific research demonstrates the existence of recent climate variation, particularly global warming. Climate prediction models forecast that climate will change; it will become warmer, droughts will increase in number and severity, and extreme climate events will recur often—desiccating aridity, extremely wet, unusually warm, or even frigid at times. However, the global models apply to average conditions in large grids approximately 150 miles on an edge (Thorpe, 2005), and how or whether specific areas within a grid are affected is unclear. Flagstaff's climate is mentioned in the context of global change, but information is lacking on the amount and trend of changes in precipitation, snowfall, and temperature. The purpose of this report is to understand what may be happening to Flagstaff's climate by reviewing local climate history. Flagstaff is in north-central Arizona south of San Francisco Mountain, which reaches 12,633 feet, the highest in Arizona (fig. 1). At 6,900 feet, surrounded by ponderosa pine forest, Flagstaff enjoys a four-season climate; winter-daytime temperatures are cool, averaging 45 degrees (Fahrenheit). Summer-daytime temperatures are comfortable, averaging 80 degrees, which is pleasant compared with nearby low-elevation deserts. Flagstaff's precipitation averages 22-inches per year with a range of 9 to 39 inches. Snowfall occurs each season, averaging 97 inches annually. This report, written for the non-technical reader, interprets climate variation at Flagstaff as observed at the National Weather Service (NWS) station at Pulliam Field (or Airport), a first-order weather station staffed by meteorologists (Staudenmaier and others, 2007). The station is on a flat-topped ridge surrounded by forest 5-miles south of Flagstaff at an elevation of 7,003 feet. Data used in this analysis are daily measurements of precipitation (including snowfall) and temperature (maximum and minimum) covering the period from 1950, when the station began operation, through spring 2007. Conversations with Byron Peterson and Michael Staudenmaier of the NWS helped us understand the difficulties of collecting consistent weather data, operation of the station, and Flagstaff's climate. Weather is the daily or even instantaneous state of temperature and precipitation. Climate is the average or accumulation of these parameters over longer time scales such as a week, month, or year. Seasonal (winter, spring, summer, and fall) and annual averages of temperature and accumulated precipitation describe the temporal variation of Flagstaff's climate, which is shown graphically with time series (figs. 2, 4, 6, 8-15). These plots show precipitation or temperature on the ordinate plotted against time on the abscissa, which is a year for annually repeating data or the year of a particular season. The plots reveal changing patterns of precipitation and temperature related to droughts, wet episodes, and rising temperatures.

Arizona↗

USGS2008

Influence of the Houma Navigation Canal on Salinity Patterns and Landscape Configuration in Coastal Louisiana

Coastal Louisiana is a dynamic and ever changing landscape. From 1956 to 2004, over 297,000 ha of Louisiana's coastal wetlands were lost because of the effects of natural and human-induced activities. Studies show that, in 2005, Hurricanes Katrina and Rita transformed over 56,200 ha of wetlands to open water in various parts of coastal Louisiana. Besides the catastrophic hurricanes, factors such as subsidence, sea-level rise, freshwater and sediment deprivation, saltwater intrusion, the dredging of oil and gas canals, navigation canals, shoreline erosion, and herbivory are all contributors to wetland loss in Louisiana. Various scientific literatures have well described the direct impacts associated with an immediate physical conversion of habitat in coastal Louisiana; however, the indirect impacts that are subtle and operate over longer time horizons (such as salinity intrusion) have been difficult to discern. In this report, long-term influences on salinity patterns and landscape configuration are evaluated for pre- and postconstruction periods of the Houma Navigation Canal (HNC), which is located in the coastal region of southeastern Louisiana. Analysis of daily and hourly salinity data from long-term data collection stations within the areas surrounding the HNC indicated that there were no obvious patterns in increasing salinity levels following the completion of the canal, except for the immediate increase in salinity spikes that occurred toward the completion of its construction in 1961. Increases in salinity spikes were also observed during a severe drought in 1999-2000. Data from Bayou Grand Caillou at Dulac, however, show a longer term trend of increasing salinity levels, which is similar to the pattern observed at the Houma Water Treatment Plant. A potential explanation for these patterns is based on the dredging history of the HNC, where dates of maintenance dredging correspond fairly closely to the salinity peaks in Bayou Grand Caillou and the canal. It appears that the dredging events opened up a deeper route from the canal to Crozier and into Grand Bayou Caillou, but it also may be a result of the general breakup of the marsh in the adjacent area, which resulted in greater exchange of bay water and subsequently higher salinity levels. Although the available salinity data were insufficient to conduct statistical correlations, there was close agreement between salinity changes and specific dredging events of the HNC. A procedure for analyzing marsh landscapes, which utilizes the FRAGSTATS landscape statistical application and a two-part marsh classification system, was developed as a means of determining the connectivity and configuration of marsh and water patches within the study area. Individual landscape metrics were used to determine the percentage and rate of land change and the shifts in density, shape, and cohesiveness of water within the marsh. Wetland loss rates for coastal Louisiana and Terrebonne basin were compared to the long- and short-term loss rates of the Houma Navigation Canal study area that were quantified by using the FRAGSTATS landscape analysis method. These results suggest that the canal study area was losing land at a significantly faster rate than both the marshes of coastal Louisiana (over all periods) and the other highly degraded neighboring marshes within Terrebonne basin. Overall, 37 percent (17,625 ha) of the project area marsh was lost between 1958 and 1998. As a means of quantifying the distance and degree of influence that the HNC had on marsh degradation, a 3-km interval buffer array and comparable years of vegetation data were used to describe the changes in primary metric values across the three project dates (1958, 1968/69, and 1998). The patterns across landscape metrics varied, and it was difficult to discern direct relationships based on proximity to the canal. Even though the canal may have an influence on marsh degradation, these analyses show that the degree and d

Open-File Report↗

USGS2008

Petrographic and Vitrinite Reflectance Analyses of a Suite of High Volatile Bituminous Coal Samples from the United States and Venezuela

This report presents vitrinite reflectance and detailed organic composition data for nine high volatile bituminous coal samples. These samples were selected to provide a single, internally consistent set of reflectance and composition analyses to facilitate the study of linkages among coal composition, bitumen generation during thermal maturation, and geochemical characteristics of generated hydrocarbons. Understanding these linkages is important for addressing several issues, including: the role of coal as a source rock within a petroleum system, the potential for conversion of coal resources to liquid hydrocarbon fuels, and the interactions between coal and carbon dioxide during enhanced coalbed methane recovery and(or) carbon dioxide sequestration in coal beds.

Open-File Report↗

USGS2008

Speciation Methods Used to Assess Potential Health Effects of Toxic Metals in Environmental Materials

Assessing potential exposures to toxic metals or metalloids such as arsenic and chromium in environmental materials is important in protecting public health. The chemical form of an element in, or released from, a material is also important, since some forms, such as Cr(VI), are more toxic than others, for example, Cr(III). We have used a variety of procedures to assess potential exposures to hexavalent chromium in ash and burned soils from October 2007 southern California wildfires. Synthetic lung-fluid and de-ionized water extractions simulate release in the lungs and potential environmental releases due to rainfall. Extracts were analyzed for specific chromium and arsenic species using HPLC-ICP-MS methodology. Results indicate that the highly oxidizing environment in wildfires promotes some chromium conversion to Cr(VI), and that the caustic alkalinity of ash enhances Cr(VI) release and stability in lung fluids and rainfall.

Open-File Report↗

USGS2009

Recent subsidence and erosion at diverse wetland sites in the southeastern Mississippi Delta Plain

A prior study (U.S. Geological Survey Open-File Report 2005-1216) examined historical land- and water-area changes and estimated magnitudes of land subsidence and erosion at five wetland sites in the Terrebonne hydrologic basin of the Mississippi delta plain. The present study extends that work by analyzing interior wetland loss and relative magnitudes of subsidence and erosion at five additional wetland sites in the adjacent Barataria hydrologic basin. The Barataria basin sites were selected for their diverse physical settings and their recent (post-1978) conversion from marsh to open water. Historical aerial photography, datum-corrected marsh elevations and water depths, sediment cores, and radiocarbon dates were integrated to evaluate land-water changes in the Mississippi delta plain on both historical and geological time scales. The thickness of the organic-rich sediments (peat) and the elevation of the stratigraphic contact between peat and underlying mud were compared at marsh and open-water sites across areas of formerly continuous marsh to estimate magnitudes of recent delta-plain elevation loss caused by vertical erosion and subsidence of the wetlands. Results of these analyses indicate that erosion exceeded subsidence at most of the study areas, although both processes have contributed to historical wetland loss. Comparison of these results with prior studies indicates that subsidence largely caused rapid interior wetland loss in the Terrebonne basin before 1978, whereas erosional processes primarily caused more gradual interior wetland loss in the Barataria basin after 1978. Decadal variations in rates of relative sea-level rise at a National Ocean Service tide gage, elevation changes between repeat benchmark-leveling surveys, and GPS height monitoring at three National Geodetic Survey Continuously Operating Reference Stations indicate that subsidence rates since the early 1990s are substantially lower than those previously reported and are similar in magnitude to time-averaged subsidence rates at geological time scales. The historical decrease in land-loss rates across the Mississippi delta plain generally is consistent with the recent decrease in subsidence rates within the same region.

Louisiana↗

USGS2009

Physical, Chemical, Ecological, and Age Data and Trench Logs from Surficial Deposits at Hatch Point, Southeastern Utah

This report presents data and describes the methodology for physical, chemical and ecological measurements of sediment, soil, and vegetation, as well as age determinations of surficial deposits at Hatch Point, Canyon Rims area, Colorado Plateau, southeastern Utah. The results presented in this report support a study that examines geomorphic and soil factors that may influence boundaries between shrubland and grassland ecosystems in the study area. Shrubland ecosystems dominated by sagebrush (Artemisia tridentata) and grassland ecosystems dominated by native perennial grasses (for example, Hilaria jamesii and Sporabolis sp.) are high-priority conservation targets for the Federal Bureau of Land Management (BLM) and other resource managers because of their diversity, productivity, and vital importance as wildlife habitat. These ecosystems have been recognized as imperiled on a regional scale since at least the mid-1990s due to habitat loss (type conversions), land-use practices, and invasive exotic plants. In the Intermountain West, the exotic annual cheatgrass (Bromus tectorum) is recognized as one of the most pervasive and serious threats to the health of native sagebrush and grassland ecosystems through effects on fire regimes and resource conditions experienced by native species.

Open-File Report↗

USGS2010

A rapid method for creating qualitative images indicative of thick oil emulsion on the ocean's surface from imaging spectrometer data

This report describes a method to create color-composite images indicative of thick oil:water emulsions on the surface of clear, deep ocean water by using normalized difference ratios derived from remotely sensed data collected by an imaging spectrometer. The spectral bands used in the normalized difference ratios are located in wavelength regions where the spectra of thick oil:water emulsions on the ocean's surface have a distinct shape compared to clear water and clouds. In contrast to quantitative analyses, which require rigorous conversion to reflectance, the method described is easily computed and can be applied rapidly to radiance data or data that have been atmospherically corrected or ground-calibrated to reflectance. Examples are shown of the method applied to Airborne Visible/Infrared Imaging Spectrometer data collected May 17 and May 19, 2010, over the oil spill from the Deepwater Horizon offshore oil drilling platform in the Gulf of Mexico.

Open-File Report↗

USGS2010

Grassland birds wintering at U.S. Navy facilities in southern Texas

Grassland birds have undergone widespread decline throughout North America during the past several decades. Causes of this decline include habitat loss and fragmentation because of conversion of grasslands to cropland, afforestation in the East, brush and shrub invasion in the Southwest and western United States, and planting of exotic grass species to enhance forage production. A large number of exotic plant species, including grasses, have been introduced in North America, but most research on the effects of these invasions on birds has been limited to breeding birds, primarily those in northern latitudes. Research on the effects of exotic grasses on birds in winter has been extremely limited. This is the first study in southern Texas to examine and compare winter bird responses to native and exotic grasslands. This study was conducted during a period of six years (2003–2009) on United States Navy facilities in southern Texas including Naval Air Station–Corpus Christi, Naval Air Station–Kingsville, Naval Auxiliary Landing Field Waldron, Naval Auxiliary Landing Field Orange Grove, and Escondido Ranch, all of which contained examples of native grasslands, exotic grasslands, or both. Data from native and exotic grasslands were collected and compared for bird abundance and diversity; ground cover, vegetation density, and floristic diversity; bird and vegetation relationships; diversity of insects and arachnids; and seed abundance and diversity. Effects of management treatments in exotic grasslands were evaluated by comparing numbers and diversity of birds and small mammals in mowed, burned, and control areas. To determine bird abundance and bird species richness, birds were surveyed monthly (December–February) during the winters of 2003–2008 in transects (100 meter × 20 meter) located in native and exotic grasslands distributed at all five U.S. Navy facilities. To compare vegetation in native and exotic grasslands, vegetation characteristics were measured during 2003–2008 in the same transects used for bird surveys and included five measures of ground cover, plus estimates of plant species richness, vegetation density (visual obstruction) at two different heights, and shrub numbers. These data, plus seasonal rainfall, were then used to evaluate components of variation in native and exotic grasslands. Relations between total bird numbers and bird species richness with environmental variation in native and exotic grasslands were compared. To compare diversity of arthropods in native and exotic grasslands, insects and arachnids were collected using three different methodologies (standardized sweep-net, random sweep-net, and pitfall traps) during four seasons, (2005–2006), at Naval Air Station–Corpus Christi, Naval Auxiliary Landing Field Waldron, and Naval Air Station–Kingsville. To compare seed abundance and diversity between native and exotic grasslands, seeds were collected for two winters (2004–2006) at Naval Air Station–Corpus Christi and Naval Air Station–Kingsville. To evaluate effects of management on grassland vertebrates, abundance and diversity of birds and small mammals were estimated and compared in exotic grasses subjected to mowing, burning, or no active management (control) for one full year (2008–2009). Observations were made of 1,044 birds of 30 species in grassland transects during five winters. The Savannah Sparrow ( Passerculus sandwichensis ) was the most common bird, which, with 644 detections, accounted for 63 percent of all individuals identified to species. Meadowlarks ( Sturnella spp. ) and Le Conte’s Sparrows ( Ammodramus leconteii ) were the second (10 percent) and third (7 percent) most abundant bird species, respectively. Six of the seven most abundant species detected in grasslands were grassland species, and their numbers accounted for 87 percent of all birds, but 20 of the 30 species (67 percent) that used grasslands were not grassland species. Seven species observed in grassland transects during the study were Species of Conservation Concern: Le Conte’s Sparrow, Sedge Wren ( Cistothorus platensis ), Grasshopper Sparrow ( Ammodramus savannarum ), Long-billed Curlew ( Numenius americanus ), Sprague’s Pipit ( Anthus spragueii ), Cassin’s Sparrow ( Aimophila cassinii ), and Loggerhead Shrike ( Lanius ludovicianus ). Native grasslands consistently supported greater bird species richness than exotic grasslands. In one winter, exotic grasslands supported more birds than native grasslands. Native grasslands were determined to have more forb cover, more bare ground, and greater plant species richness than exotic grasslands, whereas exotic grasslands were characterized by more grass cover and relatively greater vegetation density during dry years. Not only did these individual measures differ between native and exotic grasslands, but components of variation also differed. In native grasslands, grass density and cover contributed more to variation, whereas in exotic grasslands, non-grass vegetation was a greater component of variation. Total bird numbers and bird species richness in native grasslands were related to the principal component that contained a measure of litter cover. Total bird numbers and bird species richness in exotic grasslands indicated no significant relationships with any of the principal components of variation. The two most common insect orders in native grasslands were Hymenoptera and Coleoptera, which accounted for 42 percent of all insects. The two most common insect orders in exotic grasslands were Hemiptera and Homoptera, which accounted for about 80 percent of all insects. Insect family richness was greater in exotic grasslands than in native grasslands in two of four seasons. Proportions of arachnid families were similar in native and exotic grasslands, but arachnid family richness was greater in exotic grasslands than in native grasslands. Abundance of seeds was greater in exotic than in native grasslands. However, seed diversity was greater in native grasslands than in exotic grasslands. Among the three types of management (mowed, burned, and control) applied to exotic grasses, birds were most abundant in the mowed area. Sedge Wrens, however, were never encountered in mowed sites. Meadowlarks were similarly abundant in all treatments, but Le Conte’s Sparrows were detected only in the control (unmanaged) area. Hispid cotton rats ( Sigmodon hispidus ) accounted for 93 percent of all rodent captures, with the number of captures peaking December through February. Hispid cotton rat numbers and total rodent numbers were greatest in control and pre-burn areas, and lowest in the mowed area. Mammal diversity, however, was greatest in the mowed habitat. Native and exotic grasslands differed essentially in all categories (bird numbers and diversity, vegetation characteristics, components of variation, diversity of insects and arachnids, and seed abundance and diversity) used to measure and compare them. This indicates that fundamental ecosystem processes have been altered after native grasslands have undergone invasion and ultimate domination by exotic grass species. Future research in Texas grassland ecosystems is essential because: 1) Texas sustains more area in grasslands than any other state or province in the Central Flyway; 2) Texas serves as the winter destination or migration pathway for hundreds of species of birds, including winter residents and Neotropical migrants; 3) ecology, distribution, and numbers of grassland birds wintering in southern latitudes of the United States remains poorly understood; and 4) climate change threatens to further accelerate advances of invading grass species.

Open-File Report↗

USGS2010

Evaluation of extraction methods for hexavalent chromium determination in dusts, ashes, and soils

One of the difficulties in performing speciation analyses on solid samples is finding a suitable extraction method. Traditional methods for extraction of hexavalent chromium, Cr(VI), in soils, such as SW846 Method 3060A, can be tedious and are not always compatible with some determination methods. For example, the phosphate and high levels of carbonate and magnesium present in the U.S. Environmental Protection Agency (USEPA) Method 3060A digestion for Cr(VI) were found to be incompatible with the High Performance Liquid Chromatography-Inductively Coupled Plasma-Mass Spectrometry (HPLC-ICP-MS) detection method used by our laboratory. Modification of Method 3060A by eliminating the use of the phosphate buffer provided improved performance with the detection method, however dilutions are still necessary to achieve good chromatographic separation and detection of Cr(VI). An ultrasonic extraction method using a 1 mM Na2CO3 - 9 mM NaHCO3 buffer solution, adapted from Occupational Safety and Health Administration (OSHA) Method ID215, has been used with good results for the determination of Cr(VI) in air filters. The average recovery obtained for BCR-545 - Welding Dust Loaded on Filter (IRMM, Belgium) using this method was 99 percent (1.2 percent relative standard deviation) with no conversion of Cr(VI) to Cr(III) during the extraction process. This ultrasonic method has the potential for use with other sample matrices, such as ashes and soils. Preliminary investigations using NIST 2701 (Hexavalent Chromium in Contaminated Soil) loaded onto quartz filters showed promising results with approximately 90 percent recovery of the certified Cr(VI) value. Additional testing has been done using NIST 2701 and NIST 2700 using different presentation methods. Extraction efficiency of bulk presentation, where small portions of the sample are added to the bottom of the extraction vessel, will be compared with supported presentation, where small portions of the sample are loaded onto a quartz filter prior to extraction. In addition, results obtained from the standard grinding preparation of NIST 2701 and NIST 2700 will be compared with micronizing to reduce particle size before extraction.

Open-File Report↗

USGS2011

Analysis of change in marsh types of coastal Louisiana, 1978-2001

Scientists and geographers have provided multiple datasets and maps to document temporal changes in vegetation types and land-water relationships in coastal Louisiana. Although these maps provide useful historical information, technological limitations prevented these and other mapping efforts from providing sufficiently detailed calculations of areal changes and shifts in habitat coverage. The current analysis of habitat change draws upon these past mapping efforts but is based on an advanced, geographic information system dataset that was created by using Landsat 5 Thematic Mapper imagery and digital orthophoto quarter quadrangles. The objective of building this dataset was to more specifically define land-water relationships over time in coastal Louisiana, and it provides the most detailed analysis of vegetation shifts to date. In the current study, we have attempted to explain these vegetation shifts by interpreting them in the context of rainfall records, data from the Palmer Drought Severity Index, and salinity data. During the 23 years we analyzed, total marsh acreage decreased, with conversion of marsh to open water. Furthermore, the general trend across coastal Louisiana was a shift to increasingly fresh marsh types. Although fresh marsh remained almost the same during the 1978-88 study period, there were greater increases during the 1988-2001 study periods. Intermediate marsh followed the same pattern, whereas brackish marsh showed a reverse (decreasing) pattern. Changes in saline (saltwater) marsh were minimal. Interpreting shifts in marsh vegetation types by using climate and salinity data provides better understanding of factors influencing these changes and, therefore, can improve our ability to make predictions about future marsh loss related to vegetation changes. Results of our study indicate that precipitation fluctuations prior to vegetation surveys impacted salinities differently across the coast. For example, a wet 6 months prior to the survey may or may not have made up for a dry period during the earlier 12 months. More research is needed to better understand rainfall periods and how they affect salinity changes. The ability to understand past dynamics and to anticipate future trends in vegetation change and related land loss in the coastal region of Louisiana is a vital part of ongoing and future efforts to conserve its critical wetland ecosystem. With the loss of marsh and resultant changes in hydrology, it is likely that changes in marsh type may show greater variation in the future, even if given only minor changes in precipitation levels.

Open-File Report↗

USGS2011

Objectives, priorities, reliable knowledge, and science-based management of Missouri River interior least terns and piping plovers

Supporting recovery of federally listed interior least tern (Sternula antillarum athalassos; tern) and piping plover (Charadrius melodus; plover) populations is a desirable goal in management of the Missouri River ecosystem. Many tools are implemented in support of this goal, including habitat management, annual monitoring, directed research, and threat mitigation. Similarly, many types of data can be used to make management decisions, evaluate system responses, and prioritize research and monitoring. The ecological importance of Missouri River recovery and the conservation status of terns and plovers place a premium on efficient and effective resource use. Efficiency is improved when a single data source informs multiple high-priority decisions, whereas effectiveness is improved when decisions are informed by reliable knowledge. Seldom will a single study design be optimal for addressing all data needs, making prioritization of needs essential. Data collection motivated by well-articulated objectives and priorities has many advantages over studies in which questions and priorities are determined retrospectively. Research and monitoring for terns and plovers have generated a wealth of data that can be interpreted in a variety of ways. The validity and strength of conclusions from analyses of these data is dependent on compatibility between the study design and the question being asked. We consider issues related to collection and interpretation of biological data, and discuss their utility for enhancing the role of science in management of Missouri River terns and plovers. A team of USGS scientists at Northern Prairie Wildlife Research Center has been conducting tern and plover research on the Missouri River since 2005. The team has had many discussions about the importance of setting objectives, identifying priorities, and obtaining reliable information to answer pertinent questions about tern and plover management on this river system. The objectives of this presentation are to summarize those conversations and to share insights about concepts that could contribute to rigorous science support for management of this river system.

Missouri River↗

USGS2012

Dissolved oxygen analysis, TMDL model comparison, and particulate matter shunting—Preliminary results from three model scenarios for the Klamath River upstream of Keno Dam, Oregon

Efforts are underway to identify actions that would improve water quality in the Link River to Keno Dam reach of the Upper Klamath River in south-central Oregon. To provide further insight into water-quality improvement options, three scenarios were developed, run, and analyzed using previously calibrated CE-QUAL-W2 hydrodynamic and water-quality models. Additional scenarios are under development as part of this ongoing study. Most of these scenarios evaluate changes relative to a "current conditions" model, but in some cases a "natural conditions" model was used that simulated the reach without the effect of point and nonpoint sources and set Upper Klamath Lake at its Total Maximum Daily Load (TMDL) targets. These scenarios were simulated using a model developed by the U.S. Geological Survey (USGS) and Watercourse Engineering, Inc. for the years 2006–09, referred to here as the "USGS model." Another model of the reach was developed by Tetra Tech, Inc. for years 2000 and 2002 to support the Klamath River TMDL process; that model is referred to here as the "TMDL model." The three scenarios described in this report included (1) an analysis of whether this reach of the Upper Klamath River would be in compliance with dissolved oxygen standards if sources met TMDL allocations, (2) an application of more recent datasets to the TMDL model with comparison to results from the USGS model, and (3) an examination of the effect on dissolved oxygen in the Klamath River if particulate material were stopped from entering Klamath Project diversion canals. Updates and modifications to the USGS model are in progress, so in the future these scenarios will be reanalyzed with the updated model and the interim results presented here will be superseded. Significant findings from this phase of the investigation include: * The TMDL analysis used depth-averaged dissolved oxygen concentrations from model output for comparison with dissolved oxygen standards. The Oregon dissolved oxygen standards do not specify whether the numeric criteria are based on depth-averaged dissolved oxygen concentration; this was an interpretation of the standards rule by the Oregon Department of Environmental Quality (ODEQ). In this study, both depth-averaged and volume-averaged dissolved oxygen concentrations were calculated from model output. Results showed that modeled depth-averaged concentrations typically were lower than volume-averaged dissolved oxygen concentrations because depth-averaging gives a higher weight to small volume areas near the channel bottom that often have lower dissolved oxygen concentrations. Results from model scenarios in this study are reported using volume-averaged dissolved oxygen concentrations. * Under all scenarios analyzed, violations of the dissolved oxygen standard occurred most often in summer. Of the three dissolved oxygen criteria that must be met, the 30-day standard was violated most frequently. Under the base case (current conditions), fewer violations occurred in the upstream part of the reach. More violations occurred in the down-stream direction, due in part to oxygen demand from the decay of algae and organic matter from Link River and other inflows. * A condition in which Upper Klamath Lake and its Link River outflow achieved Upper Klamath Lake TMDL water-quality targets was most effective in reducing the number of violations of the dissolved oxygen standard in the Link River to Keno Dam reach of the Klamath River. The condition in which point and nonpoint sources within the Link River to Keno Dam reach met Klamath River TMDL allocations had no effect on dissolved oxygen compliance in some locations and a small effect in others under current conditions. On the other hand, meeting TMDL allocations for nonpoint and point sources was predicted to be important in meeting dissolved oxygen criteria when Upper Klamath Lake and Link River also met Upper Klamath TMDL water-quality targets. * The location of greatest dissolved oxygen improvement from nutrient and organic matter reductions was downstream from point and nonpoint source inflows because time and distance are required for decay to occur and for oxygen demand to be exerted. * After assessing compliance with dissolved oxygen standards at all 102 model segments in the Link River to Keno Dam reach, it was determined that the seven locations used by ODEQ appear to be a representative subset of the reach for dissolved oxygen analysis. * The USGS and TMDL models were qualitatively compared by running both models for the 2006–09 period but preserving the essential characteristics of each, such as organic matter partitioning, bathymetric representation, and parameter rates. The analysis revealed that some constituents were not greatly affected by the differing algorithms, rates, and assumptions in the two models. Conversely, other constituents, especially organic matter, were simulated differently by the two models. Organic matter in this river system is best represented by a mixture of relatively labile particulate material and a substantial concentration of refractory dissolved material. In addition, the use of a first-order sediment oxygen demand, as in the USGS model, helps to capture the seasonal and dynamic effect of settled organic and algal material. * Simulation of shunting (diverting) particulate material away from the intake of four Klamath Project diversion canals, so that the material stayed in the river and out of the Project area, caused higher concentrations of particulate material to occur in the river. In all cases modeled, the increase in in-river particulate material also produced decreased dissolved oxygen concentrations and an increase in the number of days when dissolved oxygen standards were violated. * If particulate material were shunted back into the river at the Klamath Project diversion canals, less organic matter and nutrients would be taken into the Klamath Project area and the Lost River basin, resulting in return flows to the Klamath River via Lost River Diversion Channel that may have reduced nutrient concentrations. Model scenarios bracketing potential end-member nutrient concentrations showed that the composition of the return flows had little to no effect on dissolved oxygen compliance under simulated conditions.

Oregon↗

USGS2012

A multi-year analysis of spillway survival for juvenile salmonids as a function of spill bay operations at McNary Dam, Washington and Oregon, 2004-09

We analyzed 6 years (2004-09) of passage and survival data collected at McNary Dam to examine how spill bay operations affect survival of juvenile salmonids passing through the spillway at McNary Dam. We also examined the relations between spill bay operations and survival through the juvenile fish bypass in an attempt to determine if survival through the bypass is influenced by spill bay operations. We used a Cormack-Jolly-Seber release-recapture model (CJS model) to determine how the survival of juvenile salmonids passing through McNary Dam relates to spill bay operations. Results of these analyses, while not designed to yield predictive models, can be used to help develop dam-operation strategies that optimize juvenile salmonid survival. For example, increasing total discharge typically had a positive effect on both spillway and bypass survival for all species except sockeye salmon ( Oncorhynchus nerka ). Likewise, an increase in spill bay discharge improved spillway survival for yearling Chinook salmon ( Oncorhynchus tshawytscha ), and an increase in spillway discharge positively affected spillway survival for juvenile steelhead ( Oncorhynchus mykiss ). The strong linear relation between increased spill and increased survival indicates that increasing the amount of water through the spillway is one strategy that could be used to improve spillway survival for yearling Chinook salmon and juvenile steelhead. However, increased spill did not improve spillway survival for subyearling Chinook salmon and sockeye salmon. Our results indicate that a uniform spill pattern would provide the highest spillway survival and bypass survival for subyearling Chinook salmon. Conversely, a predominantly south spill pattern provided the highest spillway survival for yearling Chinook salmon and juvenile steelhead. Although spill pattern was not a factor for spillway survival of sockeye salmon, spill bay operations that optimize passage through the north and south spill bays maximized spillway survival for this species. Bypass survival of yearling Chinook salmon could be improved by optimizing conditions to facilitate bypass passage at night, but the method to do so is not apparent from this analysis because photoperiod was the only factor affecting bypass survival based on the best and only supported model. Bypass survival of juvenile steelhead would benefit from lower water temperatures and increased total and spillway discharge. Likewise, subyearling Chinook salmon bypass survival would improve with lower water temperatures, increased total discharge, and a uniform spill pattern.

Oregon;Washington↗

USGS2014

High-resolution swath interferometric data collected within Muskeget Channel, Massachusetts

Swath interferometric bathymetery data were collected within and around Muskeget Channel and along select nearshore areas south and east of Martha's Vineyard, Massachusetts. Data were collected aboard the U.S. Geological Survey research vessel Rafael in October and November 2010 in a collaborative effort between the U.S. Geological Survey and the Woods Hole Oceanographic Institution. This report describes the data-collection methods and -processing steps and releases the data in geospatial format. These data were collected to support an assessment of the effect on sediment transport that a tidal instream energy conversion facility would have within Muskeget Channel. Baseline bathymetry data were obtained for the Muskeget Channel area, and surveys in select areas were repeated after one month to monitor sediment transport and bedform migration.

Massachusetts↗

USGS2013

Abstracts for the October 2012 meeting on volcanism in the American Southwest, Flagstaff, Arizona

Though volcanic eruptions are comparatively rare in the American Southwest, the States of Arizona, Colorado, New Mexico, Nevada, and Utah host Holocene volcanic eruption deposits and are vulnerable to future volcanic activity. Compared with other parts of the western United States, comparatively little research has been focused on this area, and eruption probabilities are poorly constrained. Monitoring infrastructure consists of a variety of local seismic networks, and ”backbone“ geodetic networks with little integration. Emergency response planning for volcanic unrest has received little attention by either Federal or State agencies. On October 18–20, 2012, 90 people met at the U.S. Geological Survey campus in Flagstaff, Arizona, providing an opportunity for volcanologists, land managers, and emergency responders to meet, converse, and begin to plan protocols for any future activity. Geologists contributed data on recent findings of eruptive ages, eruption probabilities, and hazards extents (plume heights, ash dispersal). Geophysicists discussed evidence for magma intrusions from seismic, geodetic, and other geophysical techniques. Network operators publicized their recent work and the relevance of their equipment to volcanic regions. Land managers and emergency responders shared their experiences with emergency planning for earthquakes. The meeting was organized out of the recognition that little attention had been paid to planning for or mitigation of volcanic hazards in the American Southwest. Moreover, few geological meetings have hosted a session specifically devoted to this topic. This volume represents one official outcome of the meeting—a collection of abstracts related to talks and poster presentations shared during the first two days of the meeting. In addition, this report includes the meeting agenda as a record of the proceedings. One additional intended outcome will be greater discussion and coordination among emergency responders, geologists, geophysicists, and land managers regarding geologic hazards in the Southwest.

Arizona, Colorado, New Mexico, Nevada, Utah↗

USGS2013

Summary of science, activities, programs, and policies that influence the rangewide conservation of Greater Sage-Grouse (Centrocercus urophasianus)

The Greater Sage-Grouse, has been observed, hunted, and counted for decades. The sagebrush biome, home to the Greater Sage-Grouse, includes sagebrush-steppe and Great Basin sagebrush communities, interspersed with grasslands, salt flats, badlands, mountain ranges, springs, intermittent creeks and washes, and major river systems, and is one of the most widespread and enigmatic components of Western U.S. landscapes. Over time, habitat conversion, degradation, and fragmentation have accumulated across the entire range such that local conditions as well as habitat distributions at local and regional scales are negatively affecting the long-term persistence of this species. Historic patterns of human use and settlement of the sagebrush ecosystem have contributed to the current condition and status of sage-grouse populations. The accumulation of habitat loss, persistent habitat degradation, and fragmentation by industry and urban infrastructure, as indicated by U.S. Fish and Wildlife Service (USFWS) findings, presents a significant challenge for conservation of this species and sustainable management of the sagebrush ecosystem. Because of the wide variations in natural and human history across these landscapes, no single prescription for management of sagebrush ecosystems (including sage-grouse habitats) will suffice to guide the collective efforts of public and private entities to conserve the species and its habitat. This report documents and summarizes several decades of work on sage-grouse populations, sagebrush as habitat, and sagebrush community and ecosystem functions based on the recent assessment and findings of the USFWS under consideration of the Endangered Species Act. As reflected here, some of these topics receive a greater depth of discussion because of the perceived importance of the issue for sagebrush ecosystems and sage-grouse populations. Drawing connections between the direct effects on sagebrush ecosystems and the effect of ecosystem condition on habitat condition, and finally the connection between habitat quality and sage-grouse population dynamics remains an important goal for science, management, and conservation. This effort is necessary, despite the perception that these complicated, indirect relations are difficult to characterize and manage, and the many advances in understanding and application developed toward this end have been documented here to help inform regional planning and policy decisions.

Arizona;California;Colorado;Montana;Nebraska;Nevad↗

USGS2013

Behavior and movement of adult summer steelhead following collection and release, lower Cowlitz River, Washington, 2012--2013

Executive Summary Historically, adult summer steelhead Oncorhynchus mykiss returning to hatcheries on the lower Cowlitz River were sometimes transported and released in the river (recycled) to provide additional angling opportunity for the popular sport fishery in the basin. However, this practice has not been used in recent years because of concerns associated with interactions between hatchery fish and wild fish. Fishery managers were interested in resuming recycling but lacked information regarding effects of this practice on wild steelhead so we conducted a study during 2012–2013 to: (1) enumerate recycled steelhead that returned to the hatchery or were removed by anglers; and (2) determine if steelhead that were not removed from the river remained in the system where they could interact with wild fish. During June–August 2012, a total of 549 summer steelhead were captured at the Cowlitz Salmon Hatchery, tagged, and released downstream near the Interstate 5 Bridge. All recycled steelhead were tagged with a white Floy ® tag and opercle-punched; 109 (20 percent) of these fish also were radio-tagged. All adult steelhead that return to the hatchery were handled by hatchery staff so recycled steelhead that returned to the hatchery were enumerated daily. A creel survey and voluntary angler reports were used to determine the number of recycled steelhead that were caught by anglers. We established three fixed telemetry monitoring sites on the mainstem Cowlitz River and eight additional sites were deployed on tributaries to the lower Cowlitz River where wild winter steelhead are known to spawn. We also conducted mobile tracking from a boat during October 2012, November 2012, and January 2013 to locate radio-tagged fish. A total of 10,722 summer steelhead were captured at the Cowlitz Salmon Hatchery in 2012, which was the largest return since 2008. River flows during much of the study period were similar to 2008–2011 average flows, however, high-flow periods in July and November 2012 were nearly twice as high as the 2008–2011 average flows. We determined that 50 percent (273 fish) of the recycled steelhead returned to the hatchery and 18 percent (102 fish) of the recycled steelhead were caught by anglers. Most (243 fish; 89 percent) of the recycled steelhead that returned to the hatchery were recollected during July–August. The average elapsed time from release to recapture at the hatchery was 9 days (d) and 72 percent (182 fish) of the fish returned to the hatchery within 14 d of release. These trends were similar for recycled steelhead that were caught by anglers. Most fish were caught during July–August and the median time from release to capture was 10 d. We determined that 65 percent (70 fish) of the angler-caught fish returned to the hatchery within 14 d of release. River flows appeared to affect both hatchery returns and angler catch. The daily number of recycled steelhead that were recollected at the hatchery were low during periods when river flows were decreasing and high during periods when river flows were increasing. Conversely, daily angler catch of recycled steelhead generally was low when flows were increasing and high when flows were decreasing. We determined that 32 percent of the recycled steelhead (174 fish) were not removed from the lower Cowlitz River, based on observations from hatchery returns and angler reports, but results from the radio-tagged fish were insightful for understanding what may have happened to these fish. By comparison, we determined that 24 percent of the radio-tagged fish were not known to have been removed from the river. We determined that 12 percent of these fish were actively moving in the lower Cowlitz River during October 2012–January 2013. None of the radio-tagged fish were detected in tributaries during the study period except for a single fish that spent approximately 7 d in the Toutle River during early September. During October 2012–January 2013, 10 percent of the radio-tags from recycled steelhead were detected near popular fishing areas, and 2 percent of the radio-tagged steelhead were never detected during the study period. We suspect that a large proportion of these fish may have been harvested and not reported, or died. Detection patterns of radio-tagged steelhead showed that most fish (82 percent) moved upstream from the release site and were detected at the Trout Hatchery and the Barrier Dam sites. The median time from release to detection at these sites was 3.7 d and many of these fish made multiple trips between the two sites. Nearly one-third (29 percent) of the recycled steelhead that were detected at the Trout Hatchery and the Barrier Dam made at least two trips between the sites and some fish made as many as six trips. Radio-tagged fish that remained in the lower Cowlitz River during the spawning period (December 2012–January 2013) were observed in the river reach between the mouth of Ostrander Creek (river mile 10) and the Trout Hatchery (river mile 44). During this study, we collected data on opercle punch regrowth rates to understand the temporal effectiveness of this marking technique. We took opercle measurements for a total of 190 fish during the study. Fresh opercle punches were measured for 63 fish at the time of marking, and the remaining 127 fish were measured when fish returned to the hatchery. We determined that opercle punches remained open for about 30 d. The holes appeared to regrow slowly in the first 20 d after marking, but regrowth accelerated during the 20–30 d post-marking period. After 30 d, all opercle punches that we observed had completely closed due to tissue regrowth. Our study showed that a large proportion (68 percent) of the recycled steelhead were removed from the lower Cowlitz River. These fish primarily entered the hatchery or were caught by anglers within 14 d of release, which suggests that they present minimal risk to wild fish in the system. However, the remaining fish (32 percent) could not be accounted for, which may complicate fisheries management decisions associated with recycling summer steelhead. Findings from the radiotelemetry study suggest that unreported harvest or mortality could explain a large proportion of those fish that were not reported as having been removed from the river. Furthermore, intensive monitoring of the key spawning tributaries failed to detect a single fish during the spawning period. These findings were supported by observations from weir traps operated by the Washington Department of Fish and Wildlife. Our findings indicate that additional research may be warranted to further examine the effects of recycling hatchery summer steelhead in the lower Cowlitz River.

Washington↗