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USGS2022

A review of empirical evidence that examines the effectiveness of harvest regulation evaluations in freshwater systems: A systematic, standardized collaborative approach

Harvest regulations are important tools that fisheries professionals use to impact fish abundance, alter population size structure, and improve fishing opportunities. Fisheries professionals often assume that specialized harvest regulations will have specific effects on target fish populations, but these predictions are not always realized because theory and practice do not always match (literature indicates that predictions are not met in about half of the cases). To identify trends that can improve the future success of harvest regulations, we reviewed a representative sample of harvest regulation evaluations for inland sport fish (i.e., 62 evaluations from 41 studies). Our review revealed gaps related to quantitative predictions, evaluation duration, statistical design, researcher–manager collaboration, and data standardization. Fisheries professionals can benefit from shared and thoughtful data collection designs and protocol standardizations. These designs can transform assessment sampling into empirical regulation evaluations that provide generality across locations and time periods with similar effort and cost.

Fisheries Magazine↗

USGS2017

Overview of avian toxicity studies for the Deepwater Horizon Natural Resource Damage Assessment

The Oil Pollution Act of 1990 establishes liability for injuries to natural resources because of the release or threat of release of oil. Assessment of injury to natural resources resulting from an oil spill and development and implementation of a plan for the restoration, rehabilitation, replacement or acquisition of natural resources to compensate for those injuries is accomplished through the Natural Resource Damage Assessment (NRDA) process. The NRDA process began within a week of the Deepwater Horizon oil spill, which occurred on April 20, 2010. During the spill, more than 8500 dead and impaired birds representing at least 93 avian species were collected. In addition, there were more than 3500 birds observed to be visibly oiled. While information in the literature at the time helped to identify some of the effects of oil on birds, it was not sufficient to fully characterize the nature and extent of the injuries to the thousands of live oiled birds, or to quantify those injuries in terms of effects on bird viability. As a result, the US Fish and Wildlife Service proposed various assessment activities to inform NRDA injury determination and quantification analyses associated with the Deepwater Horizon oil spill, including avian toxicity studies. The goal of these studies was to evaluate the effects of oral exposure to 1–20 ml of artificially weathered Mississippi Canyon 252 oil kg bw -1 day -1 from one to 28 days or one to five applications of oil to 20% of the bird's surface area. It was thought that these exposure levels would not result in immediate or short-term mortality but might result in physiological effects that ultimately could affect avian survival, reproduction and health. These studies included oral dosing studies, an external dosing study, metabolic and flight performance studies and field-based flight studies. Results of these studies indicated changes in hematologic endpoints including formation of Heinz bodies and changes in cell counts. There were also effects on multiple organ systems, cardiac function and oxidative status. External oiling affected flight patterns and time spent during flight tasks indicating that migration may be affected by short-term repeated exposure to oil. Feather damage also resulted in increased heat loss and energetic demands. The papers in this special issue indicate that the combined effects of oil toxicity and feather effects in avian species, even in the case of relatively light oiling, can significantly affect the overall health of birds.

Ecotoxicology and Environmental Safety↗

USGS2011

The hypothalamus–pituitary–thyroid axis in teleosts and amphibians: Endocrine disruption and its consequences to natural populations

Teleosts and pond-breeding amphibians may be exposed to a wide variety of anthropogenic, waterborne contaminants that affect the hypothalamus-pituitary-thyroid (HPT) axis. Because thyroid hormone is required for their normal development and reproduction, the potential impact of HPT-disrupting contaminants on natural teleost and amphibian populations raises special concern. There is laboratory evidence indicating that persistent organic pollutants, heavy metals, pharmaceutical and personal care products, agricultural chemicals, and aerospace products may alter HPT activity, development, and reproduction in teleosts and amphibians. However, at present there is no evidence to clearly link contaminant-induced HPT alterations to impairments in teleost or amphibian population health in the field. Also, with the exception of perchlorate for which laboratory studies have shown a direct link between HPT disruption and adverse impacts on development and reproductive physiology, little is known about if or how other HPT-disrupting contaminants affect organismal performance. Future field studies should focus on establishing temporal associations between the presence of HPT-disrupting chemicals, the occurrence of HPT alterations, and adverse effects on development and reproduction in natural populations; as well as determining how complex mixtures of HPT contaminants affect organismal and population health.

General and Comparative Endocrinology↗

USGS2015

The challenges of remote monitoring of wetlands

Wetlands are highly productive and support a wide variety of ecosystem goods and services. Various forms of global change impose compelling needs for timely and reliable information on the status of wetlands worldwide, but several characteristics of wetlands make them challenging to monitor remotely: they lack a single, unifying land-cover feature; they tend to be highly dynamic and their energy signatures are constantly changing; and steep environmental gradients in and around wetlands produce narrow ecotones that often are below the resolving capacity of remote sensors. These challenges and needs set the context for a special issue focused on wetland remote sensing. Contributed papers responded to one of three overarching questions aimed at improving remote, large-area monitoring of wetlands: (1) What approaches and data products are being developed specifically to support regional to global long-term monitoring of wetland landscapes? (2) What are the promising new technologies and sensor/multisensor approaches for more accurate and consistent detection of wetlands? (3) Are there studies that demonstrate how remote long-term monitoring of wetland landscapes can reveal changes that correspond with changes in land cover and land use and/or changes in climate?

Remote Sensing↗

USGS2013

Tectonic map of the Circum-Pacific region, Pacific basin sheet

Circum-Pacific Map Project : The Circum-Pacific Map Project was a cooperative international effort designed to show the relationship of known energy and mineral resources to the major geologic features of the Pacific basin and surrounding continental areas. Available geologic, mineral, and energy-resource data are being complemented by new, project-developed data sets such as magnetic lineations, seafloor mineral deposits, and seafloor sediment. Earth scientists representing some 180 organizations from more than 40 Pacific-region countries are involved in this work. Six overlapping equal-area regional maps at a scale of 1:10,000,000 form the cartographic base for the project: the four Circum-Pacific Quadrants (Northwest, Southwest, Southeast, and Northeast), and the Antarctic and Arctic Sheets. There is also a Pacific Basin Sheet at a scale of 1:17,000,000. The Base Map Series and the Geographic Series (published from 1977 to 1990), the Plate-Tectonic Series (published in 1981 and 1982), the Geodynamic Series (published in 1984 and 1985), and the Geologic Series (published from 1984 to 1989) all include six map sheets. Other thematic map series in preparation include Mineral-Resources, Energy-Resources and Tectonic Maps. Altogether, more than 50 map sheets are planned. The maps were prepared cooperatively by the Circum-Pacific Council for Energy and Mineral Resources and the U.S. Geological Survey and are available from the Branch of Distribution, U. S. Geological Survey, Box 25286, Federal Center, Denver, Colorado 80225, U.S.A. The Circum-Pacific Map Project is organized under six panels of geoscientists representing national earth-science organizations, universities, and natural-resource companies. The six panels correspond to the basic map areas. Current panel chairmen are Tomoyuki Moritani (Northwest Quadrant), R. Wally Johnson (Southwest Quadrant), Ian W.D. Dalziel (Antarctic Region), vacant. (Southeast Quadrant), Kenneth J. Drummond (Northeast Quadrant), and George W. Moore (Arctic Region). Project coordination and final cartography was being carried out through the cooperation of the Office of the Chief Geologist of the U.S. Geological Survey, under the direction of General Chairman, George Gryc of Menlo Park, California. Project headquarters were located at 345 Middlefield Road, MS 952, Menlo Park, California 94025, U.S.A. The framework for the Circum-Pacific Map Project was developed in 1973 by a specially convened group of 12 North American geoscientists meeting in California. The project was officially launched at the First Circum-Pacific Conference on Energy and Mineral Resources, which met in Honolulu, Hawaii, in August 1974. Sponsors of the conference were the AAPG, Pacific Science Association (PSA), and the Coordinating Committee for Offshore Prospecting for Mineral Resources in Offshore Asian Areas (CCOP). The Circum-Pacific Map Project operates as an activity of the Circum-Pacific Council for Energy and Mineral Resources, a nonprofit organization that promotes cooperation among Circum-Pacific countries in the study of energy and mineral resources of the Pacific basin. Founded by Michel T. Halbouty in 1972, the Council also sponsors conferences, topical symposia, workshops and the Earth Science Series books. Tectonic Map Series : The tectonic maps distinguish areas of oceanic and continental crust. Symbols in red mark active plate boundaries, and colored patterns show tectonic units (volcanic or magmatic arcs, arc-trench gaps, and interarc basins) associated with active plate margins. Well-documented inactive plate boundaries are shown by symbols in black. The tectonic development of oceanic crust is shown by episodes of seafloor spreading. These correlate with the rift and drift sequences at passive continental margins and episodes of tectonic activity at active plate margins. The recognized episodes of seafloor spreading seem to reflect major changes in plate kinematics. Oceanic plateaus and other prominences of greater than normal oceanic crustal thickness such as hotspot traces are also shown. Colored areas on the continents show the ages of deformation and metamorphism of basement rocks and the emplacement of igneous rocks. Transitional tectonic (molassic) and reactivation basins are shown by a colored boundary, and if they are deformed, a colored horizontal line pattern indicates the age of deformation. Colored bands along basin boundaries indicate age of inception, and isopachs indicate thickness of platform strata on continental crust and cover on oceanic crust. Colored patterns at separated continental margins show the age of inception of rift and drift (breakup) sequences. Symbols mark folds and faults, and special symbols show volcanoes and other structural features. Affiliations are as of compilation of the data. This map was created in quadrants and then compiled together. They are the Northwest land, Northwest Marine (different compilers), Northeast, Southwest and Southeast, and parts in plate-boundary sections.

Circum-Pacific Map↗

USGS2024

The interplay of future solar energy, land cover change, and their projected impacts on natural lands and croplands in the US

Projections for deep decarbonization require large amounts of solar energy, which may compete with other land uses such as agriculture, urbanization, and conservation of natural lands. Existing capacity expansion models do not integrate land use land cover change (LULC) dynamics into projections. We explored the interaction between projected LULC, solar photovoltaic (PV) deployment, and solar impacts on natural lands and croplands by integrating projections of LULC with a model that can project future deployment of solar PV with high spatial resolution for the conterminous United States. We used scenarios of LULC projections from the Intergovernmental Panel on Climate Change Special Report on Emission Scenarios from 2010 to 2050 and two electricity grid scenarios to model future PV deployment and compared those results against a baseline that held 2010 land cover constant through 2050. Though solar PV's overall technical potential was minimally impacted by LULC scenarios, deployed PV varied by −16.5 to 11.6 % in 2050 from the baseline scenario. Total land requirements for projected PV were similar to other studies, but measures of PV impacts on natural systems depended on the underlying land change dynamics occurring in a scenario. The solar PV deployed through 2050 resulted in 1.1 %–2.4 % of croplands and 0.3 %–0.7 % of natural lands being converted to PV. However, the deepest understanding of PV impacts and interactions with land cover emerged when the complete net gains and losses from all land cover change dynamics, including PV, were integrated. For example, one of the four LULC projections allows for high solar development and a net gain in natural lands, even though PV drives a larger percentage of natural land conversion. This paper shows that integrating land cover change dynamics with energy expansion models generates new insights into trade offs between decarbonization, impacts of renewables, and ongoing land cover change.

conterminous United States↗

USGS2009

Physical and Vegetative Characteristics of a Newly Constructed Wetland and Modified Stream Reach, Tredyffrin Township, Chester County, Pennsylvania, 2000-2006

To compensate for authorized disturbance of naturally occurring wetlands and streams during roadway improvements to U.S. Highway 202 in Chester and Montgomery Counties, Pa., the Pennsylvania Department of Transportation (PennDOT) constructed 0.42 acre of emergent wetland and 0.94 acre of scrub-shrub/forested wetland and modified sections of a 1,600-foot reach of Valley Creek with woody riparian plantings and streambank-stabilization structures (including rock deflectors). In accordance with project permits and additional guidance issued by the U.S. Army Corps of Engineers, the U.S. Geological Survey (USGS), in cooperation with PennDOT, collected data from 2000 through 2006 to quantify changes in 1) the vegetation, soils, and extent of emergent and scrub-shrub/forested parts of the constructed wetland, 2) the profile, dimension, and substrate in the vicinity of rock deflectors placed at two locations within the modified stream reach, and 3) the woody vegetation within the planted riparian buffer. The data for this investigation were collected using an approach adapted from previous investigations so that technology and findings may be more easily transferred among projects with similar objectives. Areal cover by planted and non-planted vegetation growing within the emergent and scrub-shrub/forested parts of the constructed wetland exceeded 85 percent at the end of each growing season, a criterion in special condition 25c in the U.S. Army Corps of Engineers project permit. Areal cover of vegetation in emergent and scrub-shrub/forested parts of the constructed wetland exceeded 100 percent in all but one growing season. Frequent and long-lasting soil saturation favored obligate-wetland species like Typha latifolia (broadleaf cattail) and Scirpus validus (great bulrush), both of which maintained dominance in the emergent wetland throughout the study (percent cover was 20 and 78 percent, respectively, in 2006). Echinocloa crusgalli (barnyard grass), an annual invasive from Eurasia, initially established in the newly disturbed soils of the scrub-shrub/forested wetland (areal cover was 56 percent in 2000), but by 2002, E. crusgalli was not growing in any sample plots and other species including Agrostis stolonifera (creeping bent grass), Festuca rubra (red fescue), Cornus spp. (dogwood species), and Salix nigra (black willow) were becoming more common. Sal. nigra contributed 30-percent cover in the scrub-shrub/forested wetland part by fall 2003. Rapid colonization of this species in subsequent years increased annual cover through 2006, when 15- to 25-foot tall Sal. nigra trees dominated the tree/shrub stratum (48 percent of the areal cover in 2006). The understory of the scrub-shrub/forested wetland was mostly shaded because of the canopy of Sal. nigra trees. Herbaceous species growing under and near the margins of the canopy included Ag. stolonifera and Ty. latifolia (29- and 23-percent areal cover, respectively). Flows in Valley Creek are responsible for transporting sediment and shaping the channel. Annual mean streamflow during the period the modified stream reach was monitored ranged from 15.2 cubic feet per second (ft3/s) in the 2002 water year to 53.0 ft3/s in the 2004 water year. This is a range of about 55 percent lower to 58 percent higher than the annual mean streamflow for the period of record. Despite the variability in streamflow, longitudinal profiles surveyed near rock deflectors in two short (100-foot) reaches within the modified stream reach maintained a constant slope throughout the monitoring period, most likely because of the presence of bedrock control. Cross-section geometry in the upstream reach was virtually unchanged during the monitoring period but 10 feet of bank migration was measured downstream, leaving the rock deflectors in mid-stream. As indicated by the change in channel morphology at the downstream reach, it is apparent that the rock deflectors were ineffective at adequately protecting the bank

Scientific Investigations Report↗

USGS1981

Procedures for the use of aircraft in wildlife biotelemetry studies

This is a report on the state of the art methodology and on questions that arise while one is preparing to use aircraft in a biotelemetry study. In general the first step in preparing to mount an antenna on an aircraft is to consult with a certified aircraft mechanic. Aircraft certification is discussed to provide background information concerning the role of the Federal Aviation Administration (FAA) in regulating the use of biotelemetry antennas on aircraft. However, approval of any specific design of antenna mount rests with local FAA authority. Airplane and helicopter antenna attachments are described. Performance of the receiving antenna system is discussed with emphasis on how variables as aircraft type and antenna configuration may influence reception. The side-looking vs. front-looking antenna configuration and the VHF vs. HF frequency band are generally recommended for most aerial tracking studies. Characteristics of receivers, transmitters, and antennas that might influence tracking are discussed. Specific topics such as calibration of receivers and transmitter quality control are considered. Suggestions in preparing for and conducting tracking flights that will improve overall efficiency and safety are presented. Search techniques, including procedures for conducting large and specific area surveys as well as methods to improve and evaluate search efficiency, are discussed. A concluding section considers special topics such as low-level operations and the use of helicopters. Diagrams of antenna mounts, equipment check-off lists, and antenna test procedures are included as appendices.

Resource Publication↗

USGS2026

From understanding to action: Integrating new and old methodologies to manage marine infectious disease

Marine diseases can have far-reaching effects on population, community and ecosystem health; however, our ability to track, predict and manage these diseases has, historically, been poor. As a result, the fields of disease ecology and epidemiology have developed at a slower pace for marine than terrestrial systems [ 1 ]. New methodologies, including genomic tools for diagnostics [ 2 , 3 ], transcriptomic tools for measuring host and pathogen responses to infection (e.g. [ 4 , 5 ]), regional oceanic modelling systems that estimate environmental conditions influencing pathogen dispersal and disease progression [ 6 ], artificial intelligence methods for quantifying pathology from images (e.g. [ 7 ]) and advanced disease modelling techniques [ 8 , 9 ] are precipitating a rapid increase in our understanding of marine pathosystems. In 2016, these efforts led to the first special issue of Philosophical Transactions of the Royal Society B ( Marine diseases, volume 371, issue 1689) focused entirely on marine disease ecology and evolution, and in 2020, the first book, Marine disease ecology, was devoted to this topic [ 10 ]. This special issue, focused on marine disease management , is being published a decade after the first Philosophical Transactions special issue on marine diseases. The shift to a management focus reflects an urgent need for management strategies to address high-impact diseases and the rapid methodological advances that have resulted. The papers included in this issue demonstrate the value of combining classical approaches (e.g. routine disease surveillance, reductionistic pathogen challenge trials, rapid throughput diagnostics) with cutting-edge technologies (e.g. high-resolution oceanographic models, Bayesian models, replicated transcriptomic studies) to identify drivers of disease, quantify impacts and suggest management strategies.

Philosophical Transactions of the Royal Society, S↗

USGS2019

Insect herbivores on urban native oak trees

Oak trees host an amazing diversity of insects, many of which specialize on Quercus species. Oak species and genotypes are commonly planted far from where an acorn was produced. Urban plantings, restoration sites, and plantings anticipating climate change each cause this to happen. What evidence exists that provenance of oak plantings affects herbivores such as galls and leaf miners? And what other factors, such as weather, predators, urban forestry, and geographic isolation affect the populations of these insects? I present evidence from studies of oaks conducted at different scales. Provenance matters to herbivores - but predominantly at large genetic scales. Aspects of the urban environment can help some herbivores of oak trees but hurt others. Predators are of key importance to populations of gall wasps and leaf miners, and isolated trees can maintain a great diversity of galls and miners. Creating habitat for oak herbivores (at least the ones that do not kill trees) can be a great benefit of planting native oaks, and many of those insects are nearly as charismatic as their host trees!

International Oaks↗

USGS2012

Status of groundwater quality in the California Desert Region, 2006-2008: California GAMA Priority Basin Project

Groundwater quality in six areas in the California Desert Region (Owens, Antelope, Mojave, Coachella, Colorado River, and Indian Wells) was investigated as part of the Priority Basin Project of the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The GAMA Priority Basin Project is being conducted by the California State Water Resources Control Board in collaboration with the U.S. Geological Survey (USGS) and the Lawrence Livermore National Laboratory. The six Desert studies were designed to provide a spatially unbiased assessment of the quality of untreated groundwater in parts of the Desert and the Basin and Range hydrogeologic provinces, as well as a statistically consistent basis for comparing groundwater quality to other areas in California and across the Nation. Samples were collected by the USGS from September 2006 through April 2008 from 253 wells in Imperial, Inyo, Kern, Los Angeles, Mono, Riverside, and San Bernardino Counties. Two-hundred wells were selected using a spatially distributed, randomized grid-based method to provide a spatially unbiased representation of the study areas (grid wells), and fifty-three wells were sampled to provide additional insight into groundwater conditions (additional wells). The status of the current quality of the groundwater resource was assessed based on data from samples analyzed for volatile organic compounds (VOCs), pesticides, and inorganic constituents such as major ions and trace elements. Water-quality data from the California Department of Public Health (CDPH) database also were incorporated in the assessment. The status assessment is intended to characterize the quality of untreated groundwater resources within the primary aquifer systems of the Desert Region, not the treated drinking water delivered to consumers by water purveyors. The primary aquifer systems (hereinafter, primary aquifers) in the six Desert areas are defined as that part of the aquifer corresponding to the perforation intervals of wells listed in the CDPH database. Relative-concentrations (sample concentration divided by the benchmark concentration) were used as the primary metric for evaluating groundwater quality for those constituents that have Federal and (or) California benchmarks. A relative-concentration (RC) greater than (>) 1.0 indicates a concentration above a benchmark, and an RC less than or equal to (≤) 1.0 indicates a concentration equal to or below a benchmark. Organic and special-interest constituent RCs were classified as “low” (RC ≤ 0.1), “moderate” (0.1 < RC ≤ 1.0), or “high” (RC > 1.0). Inorganic constituent RCs were classified as “low” (RC ≤ 0.5), “moderate” (0.5 < RC ≤ 1.0), or “high” (RC > 1.0). A lower threshold value RC was used to distinguish between low and moderate RCs for organic constituents because these constituents are generally less prevalent and have smaller RCs than inorganic constituents. Aquifer-scale proportion was used as the primary metric for evaluating regional-scale groundwater quality. High aquifer-scale proportion was defined as the percentage of the area of the primary aquifers with an RC greater than 1.0 for a particular constituent or class of constituents; percentage is based on an areal rather than a volumetric basis. Moderate and low aquifer-scale proportions were defined as the percentage of the primary aquifers with moderate and low RCs, respectively. Two statistical approaches—grid-based and spatially weighted—were used to evaluate aquifer-scale proportions for individual constituents and classes of constituents. Grid-based and spatially weighted estimates were comparable in the Desert Region (within 90 percent confidence intervals). The status assessment determined that one or more inorganic constituents with health-based benchmarks had high RCs in 35.4 percent of the Desert Region’s primary aquifers, moderate RCs in 27.4 percent, and low RCs in 37.2 percent. The inorganic constituents with health-based benchmarks having the largest high aquifer-scale proportions were arsenic (17.8 percent), boron (11.4 percent), fluoride (8.9 percent), gross-alpha radioactivity (6.6 percent), molybdenum (5.7 percent), strontium (3.7 percent), vanadium (3.6 percent), uranium (3.2 percent), and perchlorate (2.4 percent). Inorganic constituents with non-health-based benchmarks were also detected at high RCs in 18.6 percent and at moderate RCs in 16.0 percent of the Desert Region’s primary aquifers. In contrast, organic constituents had high RCs in only 0.3 percent of the Desert Region’s primary aquifers, moderate in 2.0 percent, low in 48.0 percent, and were not detected in 49.7 percent of the primary aquifers in the Desert Region. Of 149 organic constituents analyzed for all six study areas, 42 constituents were detected. Six organic constituents, carbon tetrachloride, chloroform, 1,2-dichloropropane, dieldrin, 1,2-dichloroethane, and tetrachloroethene, were found at moderate RCs in one or more of the grid wells. One constituent, N -nitrosodimethylamine, a special-interest VOC, was detected at a high RC in one well. Thirty-nine organic constituents were detected only at low concentrations. Three organic constituents were frequently detected (in more than 10 percent of samples from grid wells): chloroform, simazine, and deethylatrazine.

California↗

USGS2002

Individual foraging strategies of kleptoparasitic Roseate Terns

We describe the kleptoparasitic behavior of ten adult Roseate Terns ( Sterna dougallii ) breeding at a colony at Falkner Island, Connecticut, USA between 1995 and 1998. These birds were considered habitual kleptoparasites because they stole fish repeatedly from other terns in every year they were observed at the site. No other breeding individuals were observed attempting to steal fish during our study. Kleptoparasitic techniques included aerial piracy, ground-based attacks, and deceptive behavior, but with one exception, each individual used one method exclusively. Success varied among individuals, but overall, kleptoparasites obtained prey at a significantly higher rate than did 'honest' foragers. Eight of the ten kleptoparasites were females, suggesting a sex-biased tendency in Roseate Terns to engage in this behavior. Our observations indicate that kleptoparasitism by Roseate Terns is a specialized behavior, used regularly by only a few individuals at this breeding colony. This conclusion is consistent with a recent theoretical prediction regarding kleptoparasitism in birds.

Connecticut↗

USGS2006

Sediment mineralogy based on visible and near-infrared reflectance spectroscopy

Visible and near-infrared spectroscopy (VNIS) can be used to measure reflectance spectra (wavelength 350-2500 nm) for sediment cores and samples. A local ground-truth calibration of spectral features to mineral percentages is calculated by measuring reflectance spectra for a suite of samples of known mineralogy. This approach has been tested on powders, core plugs and split cores, and we conclude that it works well on all three, unless pore water is present. Initial VNIS studies have concentrated on determination of relative proportions of carbonate, opal, smectite and illite in equatorial Pacific sediments. Shipboard VNIS-based determination of these four components was demonstrated on Ocean Drilling Program Leg 199. ?? The Geological Society of London 2006.

Geological Society Special Publication↗

USGS1991

Topographical and geological amplification: Case studies and engineering implications

Topographical and geological amplification that occurred during past earthquakes are quantified using spectral ratios of recorded motions. Several cases are presented from the 1985 Chilean and Mexican earthquakes as well as the 1983 Coalinga (California) and 1987 Supersition Hills (California) earthquake. The strong motions recorded in Mexico City during the 1985 Michoacan earthquake are supplemented by ambient motions recorded within Mexico City to quantify the now well known resonating frequencies of the Mexico City lakebed. Topographical amplification in Canal Beagle (Chile), Coalinga and Superstition Hills (California) are quantified using the ratios derived from the aftershocks following the earthquakes. A special dense array was deployed to record the aftershocks in each case. The implications of both geological and topographical amplification are discussed in light of current code provisions. The observed geological amplifications has already influenced the code provisions. Suggestions are made to the effect that the codes should include further provisions to take the amplification due to topography into account.

Structural Safety↗

USGS2013

Hydrology and water quality of Shell Lake, Washburn County, Wisconsin, with special emphasis on the effects of diversion and changes in water level on the water quality of a shallow terminal lake

Shell Lake is a relatively shallow terminal lake (tributaries but no outlets) in northwestern Wisconsin that has experienced approximately 10 feet (ft) of water-level fluctuation over more than 70 years of record and extensive flooding of nearshore areas starting in the early 2000s. The City of Shell Lake (City) received a permit from the Wisconsin Department of Natural Resources in 2002 to divert water from the lake to a nearby river in order to lower water levels and reduce flooding. Previous studies suggested that water-level fluctuations were driven by long-term cycles in precipitation, evaporation, and runoff, although questions about the lake’s connection with the groundwater system remained. The permit required that the City evaluate assumptions about lake/groundwater interactions made in previous studies and evaluate the effects of the water diversion on water levels in Shell Lake and other nearby lakes. Therefore, a cooperative study between the City and U.S. Geological Survey (USGS) was initiated to improve the understanding of the hydrogeology of the area and evaluate potential effects of the diversion on water levels in Shell Lake, the surrounding groundwater system, and nearby lakes. Concerns over deteriorating water quality in the lake, possibly associated with changes in water level, prompted an additional cooperative project between the City and the USGS to evaluate efeffects of changes in nutrient loading associated with changes in water levels on the water quality of Shell Lake. Numerical models were used to evaluate how the hydrology and water quality responded to diversion of water from the lake and historical changes in the watershed. The groundwater-flow model MODFLOW was used to simulate groundwater movement in the area around Shell Lake, including groundwater/surface-water interactions. Simulated results from the MODFLOW model indicate that groundwater flows generally northward in the area around Shell Lake, with flow locally converging toward the lake. Total groundwater inflow to Shell Lake is small (approximately 5 percent of the water budget) compared with water entering the lake from precipitation (83 percent) and surface-water runoff (13 percent). The MODFLOW model also was used to simulate average annual hydrologic conditions from 1949 to 2009, including effects of the removal of 3 billion gallons of water during 2003–5. The maximum decline in simulated average annual water levels for Shell Lake due to the diversion alone was 3.3 ft at the end of the diversion process in 2005. Model simulations also indicate that although water level continued to decline through 2009 in response to local weather patterns (local drought), the effects of the diversion decreased after the diversion ceased; that is, after 4 years of recovery (2006–9), drawdown attributable to the diversion alone decreased by about 0.6 ft because of increased groundwater inflow and decreased lake-water outflow to groundwater caused by the artificially lower lake level. A delayed response in drawdown of less than 0.5 ft was transmitted through the groundwater-flow system to upgradient lakes. This relatively small effect on upgradient lakes is attributed in part to extensive layers of shallow clay that limit lake/groundwater interaction in the area. Data collected in the lake indicated that Shell Lake is polymictic (characterized by frequent deep mixing) and that its productivity is limited by the amount of phosphorus in the lake. The lake was typically classified as oligotrophic-mesotrophic in June, mesotrophic in July, and mesotrophic-eutrophic in August. In polymictic lakes like Shell Lake, phosphorus released from the sediments is not trapped near the bottom of the lake but is intermittently released to the shallow water, resulting in deteriorating water quality as summer progresses. Because the productivity of Shell Lake is limited by phosphorus, the sources of phosphorus to the lake were quantified, and the response in water quality to changes in phosphorus inputs were evaluated by means of eutrophication models. During 2009, the total input of phosphorus to Shell Lake was 1,730 pounds (lb), of which 1,320 lb came from external sources (76 percent) and 414 lb came from internal loading from sediments in the lake (24 percent). The largest external source was from surface-water runoff, which delivered about 52 percent of the total phosphorus load compared with about 13 percent of the water input. The second largest source was from precipitation (wetfall and dryfall), which delivered 19 percent of the load compared to about 83 percent of the water input. Contributions from septic systems and groundwater accounted for about 3 and 2 percent, respectively. Increased runoff raises water levels in the lake but does not necessarily increase phosphorus loading because phosphorus concentrations in the tributaries decline during increased flow, possibly because of shorter retention times in upstream wetlands. Phosphorus loading to the lake in 2009 represented what occurred after a series of dry years; therefore, this information was combined with data from 2011, a wet year, to estimate phosphorus loading during a range of hydrologic conditions by estimating loading from each component of the phosphorus budget for each year from 1949 to 2011. Comparisons of historical water-quality records with historical water levels and applications of a hydrodynamic model (Dynamic Lake Model, DLM) and empirical eutrophication models were used to understand how changes in water level and the coinciding changes in phosphorus loading affect the water quality of Shell Lake. DLM simulations indicate that large changes in water level (approximately 10 ft) affect the persistence of stratification in the lake. During periods with low water levels, the lake is a well-mixed, polymictic system, with water quality degrading slightly as summer progresses. During periods with high water levels, the lake is more stratified, and phosphorus from internal loading is trapped in the hypolimnion and released later in summer, which results in more extreme seasonality in water quality and better clarity in early summer. Results of eutrophication model simulations using a range in external phosphorus inputs illustrate how water quality in Shell Lake (phosphorus and chlorophyll a concentrations and Secchi depths) responds to changes in external phosphorus loading. Results indicate that a 50-percent reduction in external loading from that measured in 2009 would be required to change phosphorus concentrations from 0.018 milligram per liter (mg/L) (measured in 2009) to 0.012 mg/L (estimated for the mid-1800s from analysis of diatoms in sediment cores). Such reductions in phosphorus loading cannot be accomplished by targeting septic systems or internal loading alone because septic systems contribute only about 3 percent of the phosphorus input to the lake, and internal loading from the sediments of Shell Lake contributes only about 25 percent of phosphorus input. Complete elimination of phosphorus from septic systems and internal loading would decrease the phosphorus concentrations in the lake by 0.003–0.004 mg/L. Therefore, reducing phosphorus concentration in the lake more than by 0.004 mg/L requires decreasing phosphorus loading from surface-water contributions, primarily runoff to the lake. Reconstructed changes in water quality from 1860 to 2010, based on changes in the diatom communities archived in the sediments and eutrophication model simulations, suggest that anthropogenic changes in the watershed (sawmill construction in 1881; the establishment of the village of Shell Lake; and land-use changes in the 1920s, including increased agriculture) had a much larger effect on water quality than the natural changes associated with fluctuations in water level. Although the effects of natural changes in water level on water quality appear to be small, changes in water level do have a modest effect on water quality, primarily manifested as small improvements during higher water levels. Fluctuations in water level, however, have a larger effect on the seasonality of water-quality patterns, with better water quality, especially increased Secchi depths, in early summer during years with high water levels.

Wisconsin↗

USGS2019

The future is now: Amplicon sequencing and sequence capture usher in the conservation genomics era

The genomics revolution has initiated a new era of population genetics where genome-wide data are frequently used to understand complex patterns of population structure and selection. However, the application of genomic tools to inform management and conservation has been somewhat rare outside a few well studied species. Fortunately, two recently developed approaches, amplicon sequencing and sequence capture, have the potential to significantly advance the field of conservation genomics. Here, amplicon sequencing refers to highly multiplexed PCR followed by high-throughput sequencing (e.g., GTseq), and sequence capture refers to using capture probes to isolate loci from reduced-representation libraries (e.g., Rapture). Both approaches allow sequencing of thousands of individuals at relatively low costs, do not require any specialized equipment for library preparation, and generate data that can be analyzed without sophisticated computational infrastructure. Here, we discuss the advantages and disadvantages of each method and provide a decision framework for geneticists who are looking to integrate these methods into their research programme. While it will always be important to consider the specifics of the biological question and system, we believe that amplicon sequencing is best suited for projects aiming to genotype <500 loci on many individuals (>1,500) or for species where continued monitoring is anticipated (e.g., long-term pedigrees). Sequence capture, on the other hand, is best applied to projects including fewer individuals or where >500 loci are required. Both of these techniques should smooth the transition from traditional genetic techniques to genomics, helping to usher in the conservation genomics era.

Molecular Ecology Resources↗

USGS2003

Distinguishing palagonitized from pedogenically-altered basaltic Hawaiian tephra: Mineralogical and geochemical criteria

Palagonitization is a common, but imperfectly defined process that greatly modifies the physical and chemical properties of glassy basaltic tephra deposited in subaquatic/subglacial environments on Earth and perhaps Mars. It also results in textures and mineralogies that are distinct from other forms of (mainly pedogenic) low temperature alteration. Specifically, the process of palagonitization (1) initially results in the formation of 'palaginitized glass', a quasi- or nano-crystalline, rind-like material that contains smectite, as well as lesser amounts of other clays (e.g. serpentine), and (2) eventually results in consolidation of tephra, mediated through the accretion of palagonitized glass and later- formed authigenic cements. Conversely, pedogenic weathering of glassy basaltic tephra is characterized by disaggregation of tephra, and formation of a wide range of pedogenic products, including layer silicates (although not primarily smectite), short-range-order aluminosilicates and oxyhydroxides, whose composition reflects the intensity of the weathering environment. These mineralogical and textural properties can be readily recognized through a variety of techniques including electron microscopy/microprobe analysis, reflectance spectroscopy, X-ray diffraction and soil chemistry. Analyses of samples collected from the summit regions of Kilauea and Mauna Kea volcanoes on the island of Hawaii are presented here in order to illustrate differences between palagonitization and pedogenic weathering of glassy basaltic tephra. In the young Hawaiian tephras studied, palagonitization has occurred in response to hydrothermal activity shortly after deposition. Although some, non-hydrothermally affected tephras may eventually become palagonitized, those that have been strongly desilicated by intense pedogenic weathering will probably never become palagonitized.

Geological Society Special Publication↗

USGS2014

Changes in vegetation and biological soil crust communities on sand dunes stabilizing after a century of grazing on San Miguel Island, Channel Island National Park, California

San Miguel Island is the westernmost of the California Channel Islands and one of the windiest areas on the west coast of North America. The majority of the island is covered by coastal sand dunes, which were stripped of vegetation and subsequently mobilized due to droughts and sheep ranching during the late 19th century and early 20th century. Since the removal of grazing animals, vegetation and biological soil crusts have once again stabilized many of the island's dunes. In this study, historical aerial photographs and field surveys were used to develop a chronosequence of the pattern of change in vegetation communities and biological soil crust levels of development (LOD) along a gradient of dune stabilization. Historical aerial photographs from 1929, 1954, 1977, and 2009 were georeferenced and used to delineate changes in vegetation canopy cover and active (unvegetated) dune extent among 5 historical periods (pre-1929, 1929–1954, 1954–1977, 1977–2009, and 2009–2011). During fieldwork, vegetation and biological soil crust communities were mapped along transects distributed throughout San Miguel Island's central dune field on land forms that had stabilized during the 5 time periods of interest. Analyses in a geographic information system (GIS) quantified the pattern of changes that vegetation and biological soil crust communities have exhibited on the San Miguel Island dunes over the past 80 years. Results revealed that a continuing increase in total vegetation cover and a complex pattern of change in vegetation communities have taken place on the San Miguel Island dunes since the removal of grazing animals. The highly specialized native vascular vegetation (sea rocket, dunedelion, beach-bur, and locoweed) are the pioneer stabilizers of the dunes. This pioneer community is replaced in later stages by communities that are dominated by native shrubs (coastal goldenbush, silver lupine, coyote-brush, and giant coreopsis), with apparently overlapping or cyclical succession pathways. Many of the dunes that have been stabilized the longest (since before 1929) are dominated by exotic grasses. Stands of biological soil crusts (cyanobacteria) are found only on dunes where vascular vegetation is already present. Biological soil crusts are not found on dunes exhibiting a closed vascular plant canopy, which may indicate that the role of soil crusts in dune stabilization on the island is transitory. Particle-size analyses of soil samples from the study area reveal that higher biological soil crust LOD is positively correlated with increasing fine grain content. The findings indicate that changes in vegetation communities may be the most rapid at earlier and later stages of dune stabilization and that regular monitoring of dunes may help to identify the interactions between vegetation and soil crusts, as well as the potential transitions between native and exotic plant communities.

California↗