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USGS2009

NBII-SAIN Data Management Toolkit

The Strategic Plan for the U.S. Geological Survey Biological Informatics Program (2005-2009) recognizes the need for effective data management: Though the Federal government invests more than $600 million per year in biological data collection, it is difficult to address these issues because of limited accessibility and lack of standards for data and information...variable quality, sources, methods, and formats (for example observations in the field, museum specimens, and satellite images) present additional challenges. This is further complicated by the fast-moving target of emerging and changing technologies such as GPS and GIS. Even though these technologies offer new solutions, they also create new informatics challenges (Ruggiero and others, 2005). The USGS National Biological Information Infrastructure program, hereafter referred to as NBII, is charged with the mission to improve the way data and information are gathered, documented, stored, and accessed. The central objective of this project is a direct reflection of the purpose of NBII as described by John Mosesso, Program Manager of the U.S. Geological Survey-Biological Informatics Program-GAP Analysis: At the outset, the reason for bringing about NBII was that there were significant amounts of data and information scattered all over the U.S., not accessible, in incompatible formats, and that NBII was tasked with addressing this problem...NBII's focus is to pull data together that truly matters to someone or communities. Essentially, the core questions are: 1) what are the issues, 2) where is the data, and 3) how can we make it usable and accessible (John Mosesso, U.S. Geological Survey, oral commun., 2006). Redundancy in data collection can be a major issue when multiple stakeholders are involved with a common effort. In 2001 the U.S. General Accounting Office (USGAO) estimated that about 50 percent of the Federal government's geospatial data at the time was redundant. In addition, approximately 80 percent of the cost of a spatial information system is associated with spatial data collection and management (U.S. General Accounting Office, 2003). These figures indicate that the resources (time, personnel, money) of many agencies and organizations could be used more efficiently and effectively. Dedicated and conscientious data management coordination and documentation is critical for reducing such redundancy. Substantial cost savings and increased efficiency are direct results of a pro-active data management approach. In addition, details of projects as well as data and information are frequently lost as a result of real-world occurrences such as the passing of time, job turnover, and equipment changes and failure. A standardized, well documented database allows resource managers to identify issues, analyze options, and ultimately make better decisions in the context of adaptive management (National Land and Water Resources Audit and the Australia New Zealand Land Information Council on behalf of the Australian National Government, 2003). Many environmentally focused, scientific, or natural resource management organizations collect and create both spatial and non-spatial data in some form. Data management appropriate for those data will be contingent upon the project goal(s) and objectives and thus will vary on a case-by-case basis. This project and the resulting Data Management Toolkit, hereafter referred to as the Toolkit, is therefore not intended to be comprehensive in terms of addressing all of the data management needs of all projects that contain biological, geospatial, and other types of data. The Toolkit emphasizes the idea of connecting a project's data and the related management needs to the defined project goals and objectives from the outset. In that context, the Toolkit presents and describes the fundamental components of sound data and information management that are common to projects involving biological, geospatial, and other related data

Open-File Report↗
USGS2015

Bibliography for acid-rock drainage and selected acid-mine drainage issues related to acid-rock drainage from transportation activities

Acid-rock drainage occurs through the interaction of rainfall on pyrite-bearing formations. When pyrite (FeS 2 ) is exposed to oxygen and water in mine workings or roadcuts, the mineral decomposes and sulfur may react to form sulfuric acid, which often results in environmental problems and potential damage to the transportation infrastructure. The accelerated oxidation of pyrite and other sulfidic minerals generates low pH water with potentially high concentrations of trace metals. Much attention has been given to contamination arising from acid mine drainage, but studies related to acid-rock drainage from road construction are relatively limited. The U.S. Geological Survey, in cooperation with the Tennessee Department of Transportation, is conducting an investigation to evaluate the occurrence and processes controlling acid-rock drainage and contaminant transport from roadcuts in Tennessee. The basic components of acid-rock drainage resulting from transportation activities are described and a bibliography, organized by relevant categories (remediation, geochemical, microbial, biological impact, and secondary mineralization) is presented.

Tennessee↗
USGS1980

Index of streamflow and water quality records to September 30, 1978, Southwest Alaska

This report, which is one of a series of reports for Alaska, lists stations in southwest Alaska (fig. 1) at which streamflow and water-quality data have been collected by the U.S. Geological Survey. Most of the data referred to in this report have been published in reports of the Geological Survey. Water-quality data which were not included in those reports have been placed in the Survey's national computer storage system and are available through data-retrieval programs. Some of the older streamflow data have not been entered into the computer system. Geological Survey Water-Supply Paper (WSP) 1372 contains a summary of previously published records of monthly and annual discharges through September 1945, as well as records of daily and monthly discharges for the water years 1946-50 that had not yet been published. Water-Supply Paper 1372 also contains other stream chemical quality records collected between September 1948 and September 1950 and also some earlier records for the Yukon River at Anvik. Since 1950 data have been published in water-supply papers and a series of annual reports... Data have been published in the annual series of reports, "Water Resources Data for Alaska," since 1961 for streamflow records and 1964 for water-quality records. This index lists: continuous-record streamgaging stations, crest-stage gage and low-flow partial-record stations; daily chemical, sediment, and temperature stations; and stations where some chemical, sediment, and biological data have been collected on an intermittent basis.

Alaska↗
USGS1981

Hydrology of Area 7, Eastern Coal Province, Ohio

The U.S. Geological Survey established 24 study areas in Eastern Appalachian Coal Province to appraise the hydrology and water resources from Alabama to Pennsylvania. Chemical, physical, biological, and streamflow data were collected from 138 synoptic sites in Area 7, eastern Ohio. The data are evaluated and presented in this report. Area 7 lies within the drainage basins of Muskingum Rivers and Duck and Willis Creeks in eastern Ohio. Walhounding, Tuscarawas, and Little Muskingum, and Muskingum Rivers and Wills and Duck Creeks are the major streams draining the study area. In Ohio, surface and subsurface coal mining has altered the environment. In areas where land has been reclaimed, the environmental stress expected to be temporary. Hydrologic problems related to coal mining are erosion and sedimentation which degrade water-quality. Based on available sediment data, suspended sediment concentration were highest in abandoned mine areas, followed by currently mined and reclaimed areas, and lowest in unmined areas. Low pH, high specific conductance, high concentrations of iron, sulfate and manganese, increased sediment yields, discoloration of streambeds, limited aquatic vegetation and animal life typify streams draining areas with abandoned mines. In abandoned mine areas, the specific conductance of water ranged from 800 to 2,300 micromhos; pH ranged from 2.8 to 5.8; dissolved-iron concentrations ranged from 1,000 to 85,000 micrograms per liter; dissolved-sulfate concentrations ranged from 14 to 1,200 milligrams per liter and dissolved-manganese concentration commonly exceeded 2,000 micrograms per liter. Red and yellow coloration on the streambeds were precipitates from the hydrolysis of iron, manganese, and sulfate minerals carried into the stream channel by increased sediment erosion from abandoned coal mines. Trace metal concentrations (arsenic, cadmium, chromium, cobalt, copper, lead, mercury, selenium, and zinc) were generally low. Degradation of fish habitat is illustrated by conceptual model of the aquatic biology related to water chemistry.

Open-File Report↗
USGS1977

Physical, chemical, and biological relations of four ponds in the Hidden Water Creek strip-mine area, Powder River Basin, Wyoming

The Hidden Water Creek area in Wyoming was mined from 1944 to 1955 and abandoned. The open pits filled with water and pond-type ecosystems developed. Light was transmitted to greater depths within two control ponds located outside the mine area. The lower light transmittance in the ponds within the mined area probably was due, in part, to the greater number of phytoplankton cells. Also, unconsolidated soil material within the mine area was observed to slough off the pond banks, which could add to the concentration of suspended sediments. Dissolved oxygen concentrations were lower in the ponds within the mined area. Most of the major ions (calcium, magnesium, sulfate, and sodium) were present in greater concentrations in the ponds within the mined area. Higher concentrations of bicarbonate and total hardness were in the water within the mined area. Biological communities were less diverse and chemical concentrations fluctuated more in the mined area than in the ponds outside the mined area. (Woodard-USGS)

Water-Resources Investigations Report↗
USGS2002

Patterns of rodent abundance on open-space grasslands in relation to suburban edges

Relatively little is known about the response of grassland rodent populations to urban and suburban edges. We live-trapped rodents for three summers on 65 3.1-ha grassland plots on open space of the city of Boulder, Colorado, and compared capture rates among species according to habitat type, percentage of the 40 ha surrounding each plot that was suburbanized, and proximity to a suburban edge. Deer mice ( Peromyscus maniculatus ) and hispid pocket mice ( Chaetodipus hispidus ) were more abundant on interior than on edge plots in mixed grasslands, whereas prairie voles ( Microtus ochrogaster ) were captured more often on interior than on edge plots in tallgrass/hayfields. House mouse ( Mus musculus ) abundance did not differ between edge and interior plots. Native rodents as a group were captured more often on interior than on edge plots in both habitat types. For each native species, plots with the highest capture rates were in landscapes <10% suburbanized. We conclude that proximity to suburban landscapes had a strongly negative effect on the abundance of native rodents in open-space grasslands.

Conservation Biology↗
USGS2014

Influences of the Tamarisk Leaf Beetle ( Diorhabda carinulata ) on the diet of insectivorous birds along the Dolores River in Southwestern Colorado

We examined the effects of a biologic control agent, the tamarisk leaf beetle (Diorhabda carinulata), on native avifauna in southwestern Colorado, specifically, addressing whether and to what degree birds eat tamarisk leaf beetles. In 2010, we documented avian foraging behavior, characterized the arthropod community, sampled bird diets, and undertook an experiment to determine whether tamarisk leaf beetles are palatable to birds. We observed that tamarisk leaf beetles compose 24.0 percent (95-percent-confidence interval, 19.9-27.4 percent) and 35.4 percent (95-percent-confidence interval, 32.4-45.1 percent) of arthropod abundance and biomass in the study area, respectively. Birds ate few tamarisk leaf beetles, despite a superabundance of D. carinulata in the environment. The frequency of occurrence of tamarisk leaf beetles in bird diets was 2.1 percent (95-percent-confidence interval, 1.3- 2.9 percent) by abundance and 3.4 percent (95-percent-confidence interval, 2.6-4.2 percent) by biomass. Thus, tamarisk leaf beetles probably do not contribute significantly to the diets of birds in areas where biologic control of tamarisk is being applied.

Colorado;Utah↗
USGS1989

Methods for collection and analysis of aquatic biological and microbiological samples

The series of chapters on techniques describes methods used by the U.S. Geological Survey for planning and conducting water-resources investigations. The material is arranged under major subject headings called books and is further subdivided into sections and chapters. Book 5 is on laboratory analysis. Section A is on water. The unit of publication, the chapter, is limited to a narrow field of subject matter. "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" is the fourth chapter to be published under Section A of Book 5. The chapter number includes the letter of the section. This chapter was prepared by several aquatic biologists and microbiologists of the U.S. Geological Survey to provide accurate and precise methods for the collection and analysis of aquatic biological and microbiological samples. Use of brand, firm, and trade names in this chapter is for identification purposes only and does not constitute endorsement by the U.S. Geological Survey. This chapter supersedes "Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" edited by P.E. Greeson, T.A. Ehlke, G.A. Irwin, B.W. Lium, and K.V. Slack (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4, 1977) and also supersedes "A Supplement to-Methods for Collection and Analysis of Aquatic Biological and Microbiological Samples" by P.E. Greeson (U.S. Geological Survey Techniques of Water-Resources Investigations, Book 5, Chapter A4), Open-File Report 79-1279, 1979.

Techniques of Water-Resources Investigations↗
USGS2003

Recommendations for cowbird management in recovery efforts for the southwestern willow flycatcher

Three generations of mallard ducks (Anas platyrhynchos) were fed either a control diet or a diet containing 0.5 ppm mercury in the form of methylmercury. The levels of mercury in adult tissues and eggs remained about the same over 3 generations. The methylmercury diet had no effect on adult weights or weight changes during the reproductive season. Females fed a diet containing 0.5 ppm mercury laid a greater percentage of their eggs outside their nestboxes than did controls, and also laid fewer eggs and produced fewer ducklings. Methylmercury in the diet appeared to result in a small amount of eggshell thinning. Ducklings from parents fed methylmercury were less responsive than, controls to tape-recorded maternal calls, but were hyper-responsive to a frightening stimulus in avoidance tests; there were no significant differences in locomotor activity in an open-field test.

Studies in Avian Biology↗
USGS2006

Breeding biology and nest-site selection of red-tailed hawks in an altered desert grassland

Red-tailed Hawks (Buteo jamaicensis) have expanded their range as trees have invaded formerly-open grasslands. Desert grasslands of southern Arizona have been invaded by mesquite trees (Prosopis velutina) since Anglo-American settlement and now support a large population of Red-tailed Hawks. We studied a population of Red-tailed Hawks in an altered desert grassland in southern Arizona. Our objectives were to determine what environmental characteristics influence Red-tailed Hawk habitat selection in mesquite-invaded desert grasslands and to evaluate the habitat quality of these grasslands for Red-tailed Hawks based on nesting density, nest success, and productivity. Red-tailed Hawks had 86% (95% C.I. = 73-99) nest success and 1.82 young per breeding pair (95% C.I. = 1.41-2.23). Nesting density was 0.15 (95% CI = 0.08-0.21) breeding pairs/km2 and the mean nearest-neighbor distance was 1.95 km (95% C.I. = 1.74-2.16). Red-tailed Hawks selected nest-sites with taller nest-trees and greater tree height and cover than were available at random. Mesquite trees in desert grasslands provide abundant potential nesting structures for Red-tailed Hawks. ?? 2006 The Raptor Research Foundation, Inc.

Journal of Raptor Research↗
USGS2004

Limiting spread of a unicolonial invasive insect and characterization of seasonal patterns of range expansion

Limiting dispersal is a fundamental strategy in the control of invasive species, and in certain situations containment of incipient populations may be an important management technique. To test the feasibility of slowing the rapid spread of two Argentine ant ( Linepithema humile ) supercolonies in Haleakala National Park, Hawaii, we applied ant bait and toxicant within an experimental plot situated along a supercolony boundary. The 120×260 m plot simulated a small section of what could potentially be a 120 m wide treatment encompassing the entire expanding boundaries of both supercolonies. Foraging ant numbers at baited monitoring stations decreased sharply within two weeks after treatment, and ant spread was completely halted within the plot for at least one year. In contrast, an adjacent untreated colony boundary advanced an average of 65.2 m over the course of 1 year. Most of this spread took place in the summer and fall, at the time of highest ant abundance at bait monitoring stations, while no outward dispersal occurred during the spring and early summer. These patterns are consistent with the hypothesis that local budding dispersal in this unicolonial species stems from density dependent pressure rather than inherent founding behavior associated with mating. Based on results from this experiment, we are investigating the effectiveness of annual boundary treatments in slowing the Argentine ant invasion at Haleakala National Park. The goals of this program are to protect populations of native arthropods and to keep options open for eventual attempts at eradication.

Hawaii↗
USGS2007

Native Fish Sanctuary Project - Sanctuary Development Phase, 2007 Annual Report

Notable progress was made in 2007 toward the development of native fish facilities in the Lower Colorado River Basin. More than a dozen facilities are, or soon will be, online to benefit native fish. When this study began in 2005 no self-supporting communities of either bonytail or razorback sucker existed. Razorback suckers were removed from Rock Tank in 1997 and the communities at High Levee Pond had been compromised by largemouth bass in 2004. This project reversed that trend with the establishment of the Davis Cove native fish community in 2005. Bonytail and razorback sucker successfully produced young in Davis Cove in 2006. Bonytail successfully produced young in Parker Dam Pond in 2007, representing the first successful sanctuary established solely for bonytail. This past year, Three Fingers Lake received 135 large razorback suckers, and Federal and State agencies have agreed to develop a cooperative management approach dedicating a portion of that lake toward grow-out and (or) the establishment of another sanctuary. Two ponds at River's Edge Golf Course in Needles, California, were renovated in June and soon will be stocked with bonytail. Similar activities are taking place at Mohave Community College, Cerbat Cliffs Golf Course, Cibola High Levee Pond, Office Cove, Emerald Canyon Golf Course, and Bulkhead Cove. Recruitment can be expected as fish become sexually mature at these facilities. Flood-plain facilities have the potential to support 6,000 adult razorback suckers and nearly 20,000 bonytail if native fish management is aggressively pursued. This sanctuary project has assisted agencies in developing 15 native fish communities by identifying specific resource objectives for those sites, listing and prioritizing research opportunities and needs, and strategizing on management approaches through the use of resource-management plans. Such documents have been developed for Davis Cove, Cibola High Levee Pond, Parker Dam Pond, and Three Fingers Lake. We anticipate similar documents will be developed in the near future for River's Edge Golf Course Ponds, Office Cove, Emerald Canyon Golf Course Ponds, Bulkhead Cove, Mohave Community College, and Cerbat Cliffs Golf Course ponds as these facilities come on line or are developed in the future. The following report discusses the process that went into the development of these facilities. Sites were visited, assessed as to their suitability based on the control of nonnative predators, habitat suitability, conversion cost, logistics, geographical location, and willingness of landowners. They were then prioritized according to their suitability, cost, timely conversion, and willingness of landowners. Existing native fish facilities were included in this evaluation for their value in helping to determine physical and biological parameter ranges. This report describes the approaches that led to success, those leading to failure, and some of the biological, institutional, and management issues of implementing native fish sanctuary development.

Open-File Report↗