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Biological, habitat, and water quality conditions in the upper Merced River drainage, Yosemite National Park, California, 1993-1996

Four studies were done in the upper Merced River drainage in Yosemite National Park and nearby areas from 1993 to 1996. First, monitoring studies of benthic algae, benthic invertebrates, fish, and habitat were undertaken at sites near Happy Isles and Pohono bridges from 1993 to 1995 as part of the National Water-Quality Assessment Program of the U.S. Geological Survey. Second, an ecological survey of benthic algae, benthic invertebrates, fish, and habitat was done in the upper Merced River drainage in 1994. Third, a special study of benthic algae, habitat, and water quality was done in the reach of the Merced River within Yosemite Valley to deter-mine whether human activities were having measurable effects on the ecosystem. Fourth, baseline data on benthic algae, benthic invertebrates, and habitat were collected in 1996 at four sites, two of which were undergoing extensive streambank restoration activities. Comparisons of the baseline data with future collections could be used to assess the effects of streambank restoration on aquatic biota. The general conclusion from these studies is that water quality in the upper Merced River was very good from 1993-1996, despite high levels of human activities in some areas. Fish communities did not appear to be a useful indicator of habitat and water quality because of low species richness and the apparent importance of physical barriers in determining species distributions. Measurements of fish densities and size-distributions might be useful, but would be logistically difficult. Benthic algae and benthic invertebrates do appear to be useful in monitoring environmental conditions. Benthic algae may be more sensitive than benthic invertebrates to small environmental differences within years. Benthic algae were also more responsive than benthic invertebrates to differences in discharge between years. Thus, benthic invertebrates may be more useful in comparing environmental conditions between years, independent of discharge conditions.

Water-Resources Investigations Report

Wildlife specimen collection, preservation, and shipment

Specimens are used to provide supporting information leading to the determination of the cause of disease or death in wildlife and for disease monitoring or surveillance. Commonly used specimens for wildlife disease investigations include intact carcasses, tissues from carcasses, euthanized or moribund animals, parasites, ingested food, feces, or environmental samples. Samples from live animals or the environment (e.g., contaminated feed) in the same vicinity as a mortality event also may be helpful. The type of specimen collected is determined by availability of samples and biological objectives. Multiple fresh, intact carcasses from affected species are the most useful in establishing a cause for a mortality event. Submission of entire carcasses allows observation of gross lesions and abnormalities, as well as disease testing of multiple tissues. Samples from live animals may be more appropriate when sick animals cannot be euthanized (e.g., threatened or endangered species) or for research and monitoring projects examining disease or agents circulating in apparently healthy animals or those not exhibiting clinical signs. Samples from live animals may include collections of blood, hair, feathers, feces, or ectoparasites, or samples obtained by swabbing lesions or orifices. Photographs and videos are useful additions for recording field and clinical signs and conveying conditions at the site. Collection of environmental samples (e.g., feces, water, feed, or soil) may be appropriate when animals cannot be captured for sampling or the disease agent may persist in the environment. If lethal collection is considered necessary, biologists should refer to the policies, procedures, and permit requirements of their institution/facility and the agency responsible for species management (U.S. Fish and Wildlife Service or State natural resource agency) prior to use in the field. If threatened or endangered species are found dead, or there is evidence of illegal take, field personal should contact local wildlife law enforcement authorities immediately and prior to handling the carcass. Prior to collecting samples, it is important to determine the capabilities and submission criteria of the laboratory receiving the samples. Some laboratories may specialize in a limited number of tests, be equipped to accept only certain types of tissues (instead of entire carcasses), or specialize in particular species or group of animals (e.g., reptiles, birds, mammals). Diagnostic laboratories have specific requirements regarding preparation, labeling, and shipping of samples. Adherence to these requirements helps ensure the usefulness of any submitted specimens. Although laboratories may vary in the cost and turnaround times for diagnostic tests, some laboratories may be able to prioritize samples and accommodate accelerated time frames if communicated at the time of submission. Keeping a prepacked kit with basic carcass-collection supplies, including a paper copy of the specimen history form (available for download from the Web sites of most diagnostic laboratories), in the office or vehicle will decrease the chances of forgetting an essential item and decrease response time for arriving at an event.

Techniques and Methods

Description, instructions, and verification for Basinsoft, a computer program to quantify drainage- basin characteristics

Basinsoft is a computer program developed to utilize digital cartographic data to quantify 27 selected morphometric characteristics and optional area-weighted characteristics for a drainage basin. The programs comprising Basinsoft were written in Arc Macro Language (AML), a post-processing language written to run in ARC/INFO, a proprietary geographic information system (GIS). Basinsoft requires the generation of four source-data layers, three coverages and one lattice, representing the drainage-divide, hydrography, hypsography, and a lattice elevation model of a drainage basin, and the attribution of the three source-data layer coverages. Preprocessing of these data layers is facilitated by specialized utility AML programs. Compared to manual methods of measurement, Basinsoft significantly decreases the amount of time and effort required to quantify selected characteristics for drainage basins, particularly when a large number of drainage basins need to be processed. The automaticity of Basinsoft and its utility programs facilitate implementation of Basinsoft without requiring extensive GIS experience. Basinsoft was developed entirely using AML to ensure portability between platforms running ARC/INFO version 7.0 or later. Statistical comparison tests indicate Basinsoft quantifications are not significantly different from manual topographic-map measurements for 9 of 10 basin characteristics tested. The results also indicate that elevation contours generated by ARC/INFO from l:250,000-scale digital elevation model (DEM) data are over-generalized when compared to elevation contours shown on l:250,000-scale topographic maps, and that quantification of basin-slope thus is underestimated using DEM data. A qualitative comparison test indicated that the Basinsoft module used to quantify basin slope is valid and that differences in the quantification of basin slope are due to sourcedata differences.

Water-Resources Investigations Report

Benthic habitats and offshore geological resources of Kaloko-Honokohau National Historical Park, Hawai‘i

Kaloko-Honokōhau National Historical Park (KAHO) is one of three National Park lands located along the western coast of the Island of Hawai‘i and the only one to include submerged lands and marine resources within its official boundaries. The park was established in 1978 and is 1,160 acres in size, including 596 acres of marine area. The submerged lands are currently managed by the State of Hawaii, Department of Land and Natural Resources, Division of Aquatic Resources (DLNR-DAR). Marine resources located within KAHO include coral reef and habitat for many marine animals, including the green sea turtle and a variety of fish and invertebrates. In addition, many archeological, cultural, and recreational resources are located within the marine realm of the park. Potential threats and stressors to the modern marine environment include ground-water and surface-water contamination, invasive plants and algae, fishing pressure and use of monofilament gill nets (which can ensnare marine life or become tangled on reefs and be left behind as fishing debris), and visitor use impacts, such as scuba diving and snorkeling. Illegal dumping, oil releases, boat groundings, and other physical damage to reef resources are potential threats from users of the nearby harbor. Special issues of concern for the park include establishing baseline conditions of the offshore resources before the development of adjacent coastal lands. Until this study, only a general knowledge of the distribution of benthic habitats and the characteristics of the offshore region of Kaloko-Honokōhau National Historical Park was available. In 2003, a collaborative project between the U.S. Geological Survey (USGS) Coastal and Marine Geology Program and the National Park Service (NPS) was initiated to develop detailed benthic-habitat classification maps for the marine lands within and adjacent to the park. The intent of this project is to provide baseline maps and a Geographic Information System (GIS) database and description of the biological and geological resources of these marine lands in order to facilitate the management, interpretation, and understanding of park resources. A benthic-habitat classification map was created for the park using existing color aerial photography, Scanning Hydrographic Operational Airborne Lidar Survey (SHOALS) bathymetric data, georeferenced underwater video, and still photography. Individual habitat polygons were classified using five basic attributes: (1) major structure or substrate, (2) dominant structure, (3) major biologic cover on the substrate, (4) percentage of major biological cover, and (5) geographic zone. Additional information regarding geology, morphology, and coral species were also noted. Marine resources located within KAHO include coral reef and habitat for many marine animals, including the green sea turtle and a variety of fish and invertebrates. In addition, many archeological, cultural, and recreational resources are located within the marine realm of the park. Potential threats and stressors to the modern marine environment include ground-water and surface-water contamination, invasive plants and algae, fishing pressure and use of monofilament gill nets (which can ensnare marine life or become tangled on reefs and be left behind as fishing debris), and visitor use impacts, such as scuba diving and snorkeling. Illegal dumping, oil releases, boat groundings, and other physical damage to reef resources are potential threats from users of the nearby harbor. Special issues of concern for the park include establishing baseline conditions of the offshore resources before the development of adjacent coastal lands. Until this study, only a general knowledge of the distribution of benthic habitats and the characteristics of the offshore region of Kaloko-Honokōhau National Historical Park was available. In 2003, a collaborative project between the U.S. Geological Survey (USGS) Coastal and Marine Geology Program and the National Park Service (NPS) was initiated to develop detailed benthic-habitat classification maps for the marine lands within and adjacent to the park. The intent of this project is to provide baseline maps and a Geographic Information System (GIS) database and description of the biological and geological resources of these marine lands in order to facilitate the management, interpretation, and understanding of park resources. A benthic-habitat classification map was created for the park using existing color aerial photography, Scanning Hydrographic Operational Airborne Lidar Survey (SHOALS) bathymetric data, georeferenced underwater video, and still photography. Individual habitat polygons were classified using five basic attributes: (1) major structure or substrate, (2) dominant structure, (3) major biologic cover on the substrate, (4) percentage of major biological cover, and (5) geographic zone. Additional information regarding geology, morphology, and coral species were also noted.

Hawai'i

The Geologic Story of Mount Rainier

Ice-clad Mount Rainier, towering over the landscape of western Washington, ranks with Fuji-yama in Japan, Popocatepeti in Mexico, and Vesuvius in Italy among the great volcanoes of the world. At Mount Rainier, as at other inactive volcanoes, the ever-present possibility of renewed eruptions gives viewers a sense of anticipation, excitement, and apprehension not equaled by most other mountains. Even so, many of us cannot imagine the cataclysmic scale of the eruptions that were responsible for building the giant cone which now stands in silence. We accept the volcano as if it had always been there, and we appreciate only the beauty of its stark expanses of rock and ice, its flower-strewn alpine meadows, and its bordering evergreen forests. Mount Rainier owes its scenic beauty to many features. The broad cone spreads out on top of a major mountain range - the Cascades. The volcano rises about 7,000 feet above its 7,000-foot foundation, and stands in solitary splendor - the highest peak in the entire Cascade Range. Its rocky ice-mantled slopes above timberline contrast with the dense green forests and give Mount Rainier the appearance of an arctic island in a temperate sea, an island so large that you can see its full size and shape only from the air. The mountain is highly photogenic because of the contrasts it offers among bare rock, snowfields, blue sky, and the incomparable flower fields that color its lower slopes, shadows cast by the multitude of cliffs, ridges, canyons, and pinnacles change constantly from sunrise to sunset, endlessly varying the texture and mood of the mountain. The face of the mountain also varies from day to day as its broad snowfields melt during the summer. The melting of these frozen reservoirs makes Mount Rainier a natural resource in a practical as well as in an esthetic sense, for it ensures steady flows of water for hydroelectric power in the region, regardless of season. Seen from the Puget Sound country to the west, Mount Rainier has an unreal quality - its white summit, nearly 3 miles high, seems to float among the clouds. We share with the populace of the entire lowland a thrill as we watch skyward the evening's setting sun reddens the volcano's western snowfields. When you approach the mountain in its lovely setting, you may find something that appeals especially to you - the scenery, the wildlife, the glaciers, or the wildflowers. Or you may feel challenged to climb to the summit. Mount Rainier and its neighboring mountains have a special allure for a geologist because he visualizes the event - some ordinary, some truly spectacular - that made the present landscape. Such is the fascination of geology. A geologist becomes trained to see 'in his mind's eye' geologic events of thousands or even millions of years ago. And, most remarkable, he can 'see' these events by studying rocks in a cliff or roadcut, or perhaps by examining earthy material that looks like common soil beneath pastureland many miles away from the volcano. Our key to understanding the geology of Mount Rainier is that each geologic event can be reconstructed - or imagined - from the rocks formed at the time of the event. With this principle as our guide, we will review the geologic ancestry of this majestic volcano and learn what is behind its scenery.

Washington

Water resources of Branch County, Michigan

Branch County has abundant water resources throughout most of its area. Almost all the water used is supplied by wells that obtain water from glacial drift deposits and locally from fractures and sandy beds in the Coldwater Shale. Glacial drift in buried bedrock valleys may yield large quantities of water to wells. Well yields are generally adequate for domestic and farm supplies. Properly developed large-diameter wells tapping thick beds of sand and gravel of the glacial drift can yield up to several thousands of gallons per minute locally. The hundreds of lakes and the many perennial streams have great recreational value. They are also a large potential source of water for some supplies. For example, it is estimated that 88 billion gallons of water runs off in streams of the county in an average year, and the lakes o the county hold about 42billion gallons of water in storage. Problems of water supply to wells exist locally in some moraine and till areas of where the glacial drift is thin and the underlying bedrock yields only small quantities of water or none at all. Ground water is generally hard to very hard and often contains excessive iron. Salty water is mainly a problem in areas where bedrock is the chief source. Floods are not a serious problem largely because of the storage capacity of the lakes and the permeable materials in some stream basins. Based on measurements at eight stream sites the estimated amount of flow for 90 percent of the time ranges from 80,000 to 150,000 gallons per day per square mile of drainage area. A special study of low levels in land-locked Gilead Lake indicated that this lake is semiperched and mostly dependent upon the water table for tits levels.

Michigan

Geologic implications of gas hydrates in the offshore of India: results of the National Gas Hydrate Program Expedition 01

The Indian National Gas Hydrate Program Expedition 01 (NGHP-01) is designed to study the occurrence of gas hydrate along the passive continental margin of the Indian Peninsula and in the Andaman convergent margin, with special emphasis on understanding the geologic and geochemical controls on the occurrence of gas hydrate in these two diverse settings. The NGHP-01 expedition established the presence of gas hydrates in the Krishna-Godavari and Mahanadi Basins, and the Andaman Sea. The expedition discovered in the Krishna-Godavari Basin one of the thickest gas hydrate accumulations ever documented, in the Andaman Sea one of the thickest and deepest gas hydrate stability zones in the world, and established the existence of a fully developed gas hydrate petroleum system in all three basins. The primary goal of NGHP-01 was to conduct scientific ocean drilling/coring, logging, and analytical activities to assess the geologic occurrence, regional context, and characteristics of gas hydrate deposits along the continental margins of India. This was done in order to meet the long-term goal of exploiting gas hydrate as a potential energy resource in a cost effective and safe manner. During its 113.5-day voyage, the D/V JOIDES Resolution cored and/or drilled 39 holes at 21 sites (1 site in Kerala-Konkan, 15 sites in Krishna-Godavari, 4 sites in Mahanadi, and 1 site in the Andaman deep offshore area), penetrated more than 9250 m of sedimentary section, and recovered nearly 2850 m of core. Twelve holes were logged with logging-while-drilling (LWD) tools and an additional 13 holes were wireline logged. The science team utilized extensive on-board laboratory facilities to examine and prepare preliminary reports on the physical properties, geochemistry, and sedimentology of all the data collected prior to the end of the expedition. Samples were also analyzed in additional post-expedition shore-based studies conducted in leading laboratories around the world. One of the specific objectives of this expedition was to test gas hydrate formation models and constrain model parameters, especially those that account for the formation of concentrated gas hydrate accumulations. The necessary data for characterizing the occurrence of in situ gas hydrate, such as interstitial water chlorinities, core-derived gas chemistry, physical and sedimentological properties, thermal images of the recovered cores, and downhole measured logging data (LWD and/or conventional wireline log data), were obtained from most of the drill sites established during NGHP-01. Almost all of the drill sites yielded evidence for the occurrence of gas hydrate; however, the inferred in situ concentration of gas hydrate varied substantially from site to site. For the most part, the interpretation of downhole logging data, core thermal images, interstitial water analyses, and pressure core images from the sites drilled during NGHP-01 indicate that the occurrence of concentrated gas hydrate is mostly associated with the presence of fractures in the sediments, and in some limited cases, by coarser grained (mostly sand-rich) sediments.

Marine and Petroleum Geology

Potential hydrologic impacts of a tar-sand industry in 11 special tar sand areas in eastern Utah

About 93 percent of the Nation 's estimated 30 billion barrels of crude oil in tar sand deposits is in 11 tar-sand deposits in eastern Utah that were chosen for leasing by the Federal government. The Tar Sand Triangle area, which contains about 15 billion barrels of oil, is the largest. This area and the Sunnyside and P R Springs areas contain more than three-fourths of the Utah reserves. About 88,000 acre-feet of water per year would be required for a commercial tar-sand industry producing about 365,000 barrels per day. At this rate, most of the recoverable oil would be mined within 30 years. About 22,000 acre-feet of water per year would be required for a commercial tar-sand industry producing about 83,000 barrels per day. Impacts on local hydrology would be greatest in the Tar Sand Triangle, Sunnyside, and P R Springs areas. Impacts could be minimized with proper construction of surface facilities to decrease erosion, sediment transport, and impoundment of mining and retort water. Increases in salinity of the Colorado River at Imperial Dam, Ariz.-Calif., could be about 3 milligrams per liter, with a peak of 9 milligrams per liter, for a 365 ,000-barrel-per-day industry and less than 1 milligram per liter , with a peak of 2 milligrams per liter, for an 83 ,000-barrel-per-day industry. (USGS)

Water-Resources Investigations Report

Forest and flooding with special reference to the White River and Ouachita River basins, Arkansas

The observed response of trees to hydrologic stress and distribution of trees in relation to habitat indicate that flooding, ground-water level, soil moisture, soil factors, and drainage characteristics exert a strong influence on bottomland forest species distribution. The dominant hydrologic factor influencing the distribution of bottomland tree species is flooding. Individual tree species are distributed as a function of frequency and duration of flooding. In the lower White and Ouachita River basins, the flood plains consist of a series of terraces, progressively higher terraces having less frequent flooding and less duration of flooding, and a significantly different composition of forest tree species. The sites studied can be divided into four basic groups and several subgroups on the basis of flood characteristics. On Group I (water hickory-overcup oak) sites, flooded near annually 32 to 40 percent of the time, the dominant species are water hickory and overcup oak. On Group II (nuttall oak) sites, flooded near annually 10 to 21 percent of the time, a more varied flora exists including nuttall oak, willow oak, sweetgum, southern hackberry, and American elm. The third group (Group III or shagbark hickory-southern red oak) of sites is flooded at intervals from 2 to 12 years. This group includes southern red oak, shagbark hickory, and black gum. The presence of blackjack oak in addition to Group III species marks Group IV (not flooded in historic time). (Kosco-USGS)

Arkansas

U.S. Geological Survey environmental health science strategy — Providing environmental health science for a changing world

Executive Summary America has an abundance of natural resources. We have bountiful clean water, fertile soil, and unrivaled national parks, wildlife refuges, and public lands. These resources enrich our lives and preserve our health and wellbeing. These resources have been maintained because of our history of respect for their value and an enduring commitment to their vigilant protection. Awareness of the social, economic, and personal value of the health of our environment is increasing. The emergence of environmentally driven diseases caused by exposure to contaminants and pathogens is a growing concern worldwide. New health threats and patterns of established threats are affected by both natural and anthropogenic changes to the environment. Human activities are key drivers of emerging (new and re-emerging) health threats. Societal demands for land and natural resources, quality of life, and economic prosperity lead to environmental change. Natural earth processes, climate trends, and related climatic events will compound the environmental impact of human activities. These environmental drivers will influence exposure to disease agents, including viral, bacterial, prion, and fungal pathogens, parasites, synthetic chemicals and substances, natural earth materials, toxins, and other biogenic compounds. The U.S. Geological Survey (USGS) defines environmental health science broadly as the interdisciplinary study of relations among the quality of the physical environment, the health of the living environment, and human health. The interactions among these three spheres are driven by human activities, ecological processes, and natural earth processes; the interactions affect exposure to contaminants and pathogens and the severity of environmentally driven diseases in animals and people. This definition provides USGS with a framework for synthesizing natural science information from across the Bureau and providing it to environmental, natural resource, agricultural, and public health managers. USGS specializes in science at the environment-health interface, by characterizing the processes that affect the interaction among the physical environment, the living environment, and people, and the resulting factors that affect ecological and human exposure to disease agents. The USGS is a Federal science agency with a broad range of natural science expertise relevant to environmental health. USGS provides scientific information and tools as a scientific basis for management and policy decisionmaking. This report describes a 10-year strategy that encompasses the portfolio of USGS environmental health science. It summarizes national environmental health priorities that USGS is best suited to address, and will serve as a strategic framework for USGS environmental health science goals, actions, and outcomes for the next decade. Implementation of this strategy is intended to aid coordination of USGS environmental health activities and to provide a focal point for disseminating information to stakeholders. The “One Health” paradigm advocated by the World Health Organization (WHO; World Health Organization, 2011), and the American Veterinary Medical Association (AVMA; American Veterinary Medical Association, 2008), among others, is based on a general recognition that the health of humans, animals, and the environment are inextricably linked. Thus, successful efforts to protect that health will require increased interdisciplinary research and increased communication and collaboration among the broader scientific and health community. This strategy is built upon that paradigm.

Circular

Quality of groundwater and surface water, Wood River Valley, south-central Idaho, July and August 2012

Residents and resource managers of the Wood River Valley of south-central Idaho are concerned about the effects that population growth might have on the quality of groundwater and surface water. As part of a multi-phase assessment of the groundwater resources in the study area, the U.S. Geological Survey evaluated the quality of water at 45 groundwater and 5 surface-water sites throughout the Wood River Valley during July and August 2012. Water samples were analyzed for field parameters (temperature, pH, specific conductance, dissolved oxygen, and alkalinity), major ions, boron, iron, manganese, nutrients, and Escherichia coli (E.coli) and total coliform bacteria. This study was conducted to determine baseline water quality throughout the Wood River Valley, with special emphasis on nutrient concentrations. Water quality in most samples collected did not exceed U.S. Environmental Protection Agency standards for drinking water. E. coli bacteria, used as indicators of water quality, were detected in all five surface-water samples and in two groundwater samples collected. Some analytes have aesthetic-based recommended drinking water standards; one groundwater sample exceeded recommended iron concentrations. Nitrate plus nitrite concentrations varied, but tended to be higher near population centers and in agricultural areas than in tributaries and less populated areas. These higher nitrate plus nitrite concentrations were not correlated with boron concentrations or the presence of bacteria, common indicators of sources of nutrients to water. None of the samples collected exceeded drinking-water standards for nitrate or nitrite. The concentration of total dissolved solids varied considerably in the waters sampled; however a calcium-magnesium-bicarbonate water type was dominant (43 out of 50 samples) in both the groundwater and surface water. Three constituents that may be influenced by anthropogenic activity (chloride, boron, and nitrate plus nitrite) deviate from this pattern and show a wide distribution of concentrations in the unconfined aquifer, indicating possible anthropogenic influence. Time-series plots of historical water-quality data indicated that nitrate does not seem to be increasing or decreasing in groundwater over time; however, time-series plots of chloride concentrations indicate that chloride may be increasing in some wells. The small amount of temporal variability in nitrate concentrations indicates a lack of major temporal changes to groundwater inputs.

Idaho

The Amphibian Research and Monitoring Initiative (ARMI): 5-year report

The Amphibian Research and Monitoring Initiative (ARMI) is an innovative, multidisciplinary program that began in 2000 in response to a congressional directive for the Department of the Interior to address the issue of amphibian declines in the United States. ARMI’s formulation was cross-disciplinary, integrating U.S. Geological Survey scientists from Biology, Water, and Geography to develop a course of action (Corn and others, 2005a). The result has been an effective program with diverse, yet complementary, expertise. ARMI’s approach to research and monitoring is multiscale. Detailed investigations focus on a few species at selected local sites throughout the country; monitoring addresses a larger number of species over broader areas (typically, National Parks and National Wildlife Refuges); and inventories to document species occurrence are conducted more extensively across the landscape. Where monitoring is conducted, the emphasis is on an ability to draw statistically defensible conclusions about the status of amphibians. To achieve this objective, ARMI has instituted a monitoring response variable that has nationwide applicability. At research sites, ARMI focuses on studying species/environment interactions, determining causes of observed declines, and developing new techniques to sample populations and analyze data. Results from activities at all scales are provided to scientists, land managers, and policymakers, as appropriate. The ARMI program and the scientists involved contribute significantly to understanding amphibian declines at local, regional, national, and international levels. Within National Parks and National Wildlife Refuges, findings help land managers make decisions applicable to amphibian conservation. For example, the National Park Service (NPS) selected amphibians as a vital sign for several of their monitoring networks, and ARMI scientists provide information and assistance in developing monitoring methods for this NPS effort. At the national level, ARMI has had major exposure at a variety of meetings, including a dedicated symposium at the 2004 joint meetings of the Herpetologists’ League, the American Society of Ichthyologists and Herpetologists, and the Society for the Study of Amphibians and Reptiles. Several principal investigators have brought international exposure to ARMI through venues such as the World Congress of Herpetology in South Africa in 2005 (invited presentation by Dr. Gary Fellers), the Global Amphibian Summit, sponsored by the International Union for Conservation of Nature (IUCN) and Wildlife Conservation International, in Washington, D.C., 2005 (invited participation by Dr. P.S. Corn), and a special issue of the international herpetological journal Alytes focused on ARMI in 2004 (edited by Dr. C.K. Dodd, Jr.). ARMI research and monitoring efforts have addressed at least 7 of the 21 Threatened and Endangered Species listed by the U.S. Fish and Wildlife Service (California red-legged frog [Rana draytonii], Chiricahua leopard frog [R. chiricahuensis], arroyo toad [Bufo californicus], dusky gopher frog [Rana sevosa], mountain yellow-legged frog [R. muscosa], flatwoods salamander [Ambystoma cingulatum], and the golden coqui [Eleutherodactylus jasperi]), and 9 additional species of concern recognized by the IUCN. ARMI investigations have addressed time-sensitive research, such as emerging infectious diseases and effects on amphibians related to natural disasters like wildfire, hurricanes, and debris flows, and the effects of more constant, environmental change, like urban expansion, road development, and the use of pesticides. Over the last 5 years, ARMI has partnered with an extensive list of government, academic, and private entities. These partnerships have been fruitful and have assisted ARMI in developing new field protocols and analytic tools, in using and refining emerging technologies to improve accuracy and efficiency of data handling, in conducting amphibian disease, malformation, and environmental effects research, and in implementing a network of monitoring and research sites. Accomplishments from these endeavors include more than 40 publications on amphibian status and trends, nearly 100 publications on amphibian ecology and causes of declines, and over 30 methodological publications. Several databases have emerged as a result of ARMI and its partnerships; one, a digital atlas of ranges for all U.S. amphibian species, was used by the IUCN to display amphibian distribution maps in the Global Amphibian Assessment Project. Given the scope of ARMI and the panoply of projects, findings have had implications for policy. Investigations that demonstrate amphibian declines or illuminate causes of declines provide valuable information about habitat management, environmental effects, mechanisms for the spread of disease, and human/amphibian interfaces. This information has been made available to land managers, scientists, educators, Congress and other policymakers, and the public. The support afforded ARMI by Congress has been influential in the program’s development and success. The value of ARMI’s efforts will continue to increase as we are able to extend our studies spatially and temporally to answer critical questions with more confidence. We are using ARMI’s resources efficiently and continuing to develop innovative mechanisms for leveraging resources for maximum effectiveness during challenging financial times. This report is a 5-year retrospective of the structure, methodology, progress, and contributions to the broader scientific community that have resulted from this national USGS program. We evaluate ARMI’s success to date, with regard to the challenges faced by the program and the strengths that have emerged. We chart objectives for the next 5 years that build on current accomplishments, highlight areas meriting further research, and direct efforts to overcome existing weaknesses.

Scientific Investigations Report

Preliminary integrated geologic map databases for the United States: Digital data for the reconnaissance geologic map of the western Aleutian Islands, Alaska

The growth in the use of Geographic Information Systems (GIS) has highlighted the need for digital geologic maps that have been attributed with information about age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. This report is part of a series of integrated geologic map databases that cover the entire United States. Three national-scale geologic maps that portray most or all of the United States already exist; for the conterminous U.S., King and Beikman (1974a,b) compiled a map at a scale of 1:2,500,000, Beikman (1980) compiled a map for Alaska at 1:2,500,000 scale, and for the entire U.S., Reed and others (2005a,b) compiled a map at a scale of 1:5,000,000. A digital version of the King and Beikman map was published by Schruben and others (1994). Reed and Bush (2004) produced a digital version of the Reed and others (2005a) map for the conterminous U.S. The present series of maps is intended to provide the next step in increased detail. State geologic maps that range in scale from 1:100,000 to 1:1,000,000 are available for most of the country, and digital versions of these state maps are the basis of this product. The digital geologic maps presented here are in a standardized format as ARC/INFO Exportfiles/ and as ArcView shape files. Data tables that relate the map units to detailed lithologic and age information accompany these GIS files. The map is delivered as a set 1:250,000-scale quadrangle files. To the best of our ability, these quadrangle files are edge-matched with respect to geology. When the maps are merged, the combined attribute tables can be used directly with the merged maps to make derivative maps.

Alaska

Mitigation and enhancement techniques for the Upper Mississippi River system and other large river systems

Extensive information is provided on techniques that can reduce or eliminate the negative impact of man's activities (particularly those related to navigation) on large river systems, with special reference to the Upper Mississippi River. These techniques should help resource managers who are concerned with such river systems to establish sound environmental programs. Discussion of each technique or group of techniques include (1) situation to be mitigated or enhanced; (2) description of technique; (3) impacts on the environment; (4) costs; and (5) evaluation for use on the Upper Mississippi River Systems. The techniques are divided into four primary categories: Bank Stabilization Techniques, Dredging and Disposal of Dredged Material, Fishery Management Techniques, and Wildlife Management Techniques. Because techniques have been grouped by function, rather than by structure, some structures are discussed in several contexts. For example, gabions are discussed for use in revetments, river training structures, and breakwaters. The measures covered under Bank Stabilization Techniques include the use of riprap revetments, other revetments, bulkheads, river training structures, breakwater structures, chemical soil stabilizers, erosion-control mattings, and filter fabrics; the planting of vegetation; the creation of islands; the creation of berms or enrichment of beaches; and the control of water level and boat traffic. The discussions of Dredging and the Disposal of Dredged Material consider dredges, dredging methods, and disposal of dredged material. The following subjects are considered under Fishery Management Techniques: fish attractors; spawning structures; nursery ponds, coves, and marshes; fish screens and barriers; fish passage; water control structures; management of water levels and flows; wing dam modification; side channel modification; aeration techniques; control of nuisance aquatic plants; and manipulated of fish populations. Wildlife Management Techniques include treatments of artificial nest structures, island creation or development, marsh creation or development, greentree reservoirs and mast management, vegetation control, water level control, and revegetation.

Upper Mississippi River

Preliminary integrated geologic map databases for the United States: Digital data for the reconnaissance geologic map of the lower Yukon River region, Alaska

The growth in the use of Geographic Information Systems (GIS) has highlighted the need for digital geologic maps that have been attributed with information about age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. This report is part of a series of integrated geologic map databases that cover the entire United States. Three national-scale geologic maps that portray most or all of the United States already exist; for the conterminous U.S., King and Beikman (1974a,b) compiled a map at a scale of 1:2,500,000, Beikman (1980) compiled a map for Alaska at 1:2,500,000 scale, and for the entire U.S., Reed and others (2005a,b) compiled a map at a scale of 1:5,000,000. A digital version of the King and Beikman map was published by Schruben and others (1994). Reed and Bush (2004) produced a digital version of the Reed and others (2005a) map for the conterminous U.S. The present series of maps is intended to provide the next step in increased detail. State geologic maps that range in scale from 1:100,000 to 1:1,000,000 are available for most of the country, and digital versions of these state maps are the basis of this product. The digital geologic maps presented here are in a standardized format as ARC/INFO export files and as ArcView shape files. Data tables that relate the map units to detailed lithologic and age information accompany these GIS files. The map is delivered as a set 1:250,000-scale quadrangle files. To the best of our ability, these quadrangle files are edge-matched with respect to geology. When the maps are merged, the combined attribute tables can be used directly with the merged maps to make derivative maps.

Alaska

Preliminary integrated geologic map databases for the United States: Digital data for the reconnaissance bedrock geologic map for the northern Alaska peninsula area, southwest Alaska

he growth in the use of Geographic Information Systems (GIS) has highlighted the need for digital geologic maps that have been attributed with information about age and lithology. Such maps can be conveniently used to generate derivative maps for manifold special purposes such as mineral-resource assessment, metallogenic studies, tectonic studies, and environmental research. This report is part of a series of integrated geologic map databases that cover the entire United States. Three national-scale geologic maps that portray most or all of the United States already exist; for the conterminous U.S., King and Beikman (1974a,b) compiled a map at a scale of 1:2,500,000, Beikman (1980) compiled a map for Alaska at 1:2,500,000 scale, and for the entire U.S., Reed and others (2005a,b) compiled a map at a scale of 1:5,000,000. A digital version of the King and Beikman map was published by Schruben and others (1994). Reed and Bush (2004) produced a digital version of the Reed and others (2005a) map for the conterminous U.S. The present series of maps is intended to provide the next step in increased detail. State geologic maps that range in scale from 1:100,000 to 1:1,000,000 are available for most of the country, and digital versions of these state maps are the basis of this product. The digital geologic maps presented here are in a standardized format as ARC/INFO export files and as ArcView shape files. Data tables that relate the map units to detailed lithologic and age information accompany these GIS files. The map is delivered as a set 1:250,000-scale quadrangle files. To the best of our ability, these quadrangle files are edge-matched with respect to geology. When the maps are merged, the combined attribute tables can be used directly with the merged maps to make derivative maps.

Alaska

EAARL-B coastal topography: eastern New Jersey, Hurricane Sandy, 2012: first surface

These remotely sensed, geographically referenced elevation measurements of lidar-derived first-surface (FS) topography datasets were produced by the U.S. Geological Survey (USGS), St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida. This project provides highly detailed and accurate datasets for a portion of the New Jersey coastline beachface, acquired pre-Hurricane Sandy on October 26, and post-Hurricane Sandy on November 1 and November 5, 2012. The datasets are made available for use as a management tool to research scientists and natural-resource managers. An innovative airborne lidar system, known as the second-generation Experimental Advanced Airborne Research Lidar (EAARL-B), was used during data acquisition. The EAARL-B system is a raster-scanning, waveform-resolving, green-wavelength (532-nm) lidar designed to map nearshore bathymetry, topography, and vegetation structure simultaneously. The EAARL-B sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive lidar, down-looking red-green-blue (RGB) and infrared (IR) digital cameras, two precision dual-frequency kinematic carrier-phase GPS receivers, and an integrated miniature digital inertial measurement unit, which provide for sub-meter georeferencing of each laser sample. The nominal EAARL-B platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL-B system. The resulting data were then processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of lidar data in an interactive or batch mode. Modules for presurvey flight-line definition, flight-path plotting, lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is used routinely to create maps that represent submerged or sub-aerial topography. Specialized filtering algorithms have been implemented to determine the "bare earth" under vegetation from a point cloud of last return elevations. For more information about similar projects, please visit the Lidar for Science and Resource Management Web site.

New Jersey

EAARL coastal topography and imagery–Western Louisiana, post-Hurricane Rita, 2005: First surface

These remotely sensed, geographically referenced color-infrared (CIR) imagery and elevation measurements of lidar-derived first-surface (FS) topography datasets were produced by the U.S. Geological Survey (USGS), St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida, and the National Aeronautics and Space Administration (NASA), Wallops Flight Facility, Virginia. This project provides highly detailed and accurate datasets of a portion of the Louisiana coastline beachface, acquired post-Hurricane Rita on September 27-28 and October 2, 2005. The datasets are made available for use as a management tool to research scientists and natural-resource managers. An innovative airborne lidar instrument originally developed at the National Aeronautics and Space Administration (NASA) Wallops Flight Facility, and known as the Experimental Advanced Airborne Research Lidar (EAARL), was used during data acquisition. The EAARL system is a raster-scanning, waveform-resolving, green-wavelength (532-nanometer) lidar designed to map near-shore bathymetry, topography, and vegetation structure simultaneously. The EAARL sensor suite includes the raster-scanning, water-penetrating full-waveform adaptive lidar, a down-looking red-green-blue (RGB) digital camera, a high-resolution multispectral color-infrared (CIR) camera, two precision dual-frequency kinematic carrier-phase GPS receivers, and an integrated miniature digital inertial measurement unit, which provide for sub-meter georeferencing of each laser sample. The nominal EAARL platform is a twin-engine Cessna 310 aircraft, but the instrument may be deployed on a range of light aircraft. A single pilot, a lidar operator, and a data analyst constitute the crew for most survey operations. This sensor has the potential to make significant contributions in measuring sub-aerial and submarine coastal topography within cross-environmental surveys. Elevation measurements were collected over the survey area using the EAARL system, and the resulting data were then processed using the Airborne Lidar Processing System (ALPS), a custom-built processing system developed in a NASA-USGS collaboration. ALPS supports the exploration and processing of lidar data in an interactive or batch mode. Modules for presurvey flight-line definition, flight-path plotting, lidar raster and waveform investigation, and digital camera image playback have been developed. Processing algorithms have been developed to extract the range to the first and last significant return within each waveform. ALPS is used routinely to create maps that represent submerged or sub-aerial topography. Specialized filtering algorithms have been implemented to determine the "bare earth" under vegetation from a point cloud of last return elevations. For more information about similar projects, please visit the Lidar for Science and Resource Management Website.

Louisiana