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USGS2006

Palila Restoration: Lessons from Long-term Research

BACKGROUND The palila (Loxioides bailleui) is a member of the Hawaiian honeycreeper family of birds (Drepanidinae), which is renowned for the profusion of species - many with bizarre bills and specialized feeding habits - that radiated from a single ancestral type. Most of the 57 or so honeycreeper species are extinct, and the palila is endangered because of its high degree of dependence on the mamane tree (Sophora chrysophylla) (Figure 1) and its restricted distribution on the upper slopes of Mauna Kea (Figure 2). Three decades of research have revealed many important facts about palila, providing the foundation and impetus for conservation programs in the wild and captivity. Additionally, an ambitious public conservation campaign arose due to the land-use conflicts on Mauna Kea. Here we summarize progress in palila conservation biology and outline steps that might overcome the remaining major challenges to its recovery. We also highlight lessons learned from palila research that may help the recovery of other Hawaiian forest birds. Palila and two closely-related species on the tiny islands of Nihoa and Laysan are the last of the seed-eating honeycreeper species in the Hawaiian Islands. About a quarter of the honeycreeper species known from living and fossil specimens had finch-like bills suited mainly for eating seeds and fruits. Because of their dietary specialization, palila are vulnerable to changes in forest size and quality, as was also likely the case for extinct species of seed specialists. Palila and many other forest bird species were once distributed in dry, lowland forests. Fossil records indicate that palila also occurred in the lowlands of O`ahu and Kaua`i until human settlement of those islands. However, because lowland habitats have been highly modified by humans and because mamane occurs today primarily at high elevation, palila are the only native bird species found exclusively in dry, subalpine habitat (2000?2850 m). Similar to other feeding specialists, palila lay few eggs, raise few young each year, and take a relatively long time to complete the nesting cycle. Low rates of reproduction result in low rates of population growth and low potential for recovery from disturbances. Long-term studies of palila offer important insights into the conservation biology of all Hawaiian forest bird species, particularly feeding specialists like the palila. Palila face many challenges common to both generalist and specialist Hawaiian honeycreeper species. Habitat loss and degradation, as well as introduced avian diseases, have reduced their numbers and limited their distribution to a very small portion of their historic range. Introduced mammals prey on palila, while alien insects reduce caterpillars that are particularly important in the diet of nestlings. Securing legal protection and funding for palila restoration has been challenging. Understanding how the palila has avoided extinction can help managers plan its recovery, and better design recovery plans for species with different feeding strategies in other habitats.

Fact Sheet↗

USGS1915

Contributions to the stratigraphy of southwestern Colorado

In the course of field work of the United States Geological Survey in the San Juan region of Colorado observations have been made in the last three seasons that considerably extend our knowledge of the great stratigraphic break below the La Plata sandstone, which is currently assumed to be of Jurassic age. The new data pertain partly to the relations existing in the Gunnison Valley, north of the San Juan Mountains, where the unconformity marking this break was already known at certain places, and partly to the conditions in the Piedra Valley, on the south side of the mountains, where the unconformity had not before been noted. The Piedra Valley is of special interest, and it seems well to call attention to the relations observed even though they were examined only in a reconnaissance. The first part of this paper is devoted to the evidence of the overlap of the La Plata sandstone; the second to the stratigraphic relations in the Piedra Valley. The section of sedimentary formations in Piedra Canyon is of much interest because none of the pre-La Plata formations are known east of this locality on the south side of the San Juan Mountains. Most of these formations exhibit a notably different facies where they reappear from beneath the overlying beds at their nearest exposures in New Mexico, southeast of the Piedra Valley. It is believed that the character of the formations in the Piedra section should be recorded for the benefit of geologists who may be studying the Paleozoic and Mesozoic rocks of New Mexico, and accordingly the second part of the paper presents details of the structure and the stratigraphic section of Piedra Valley.

Colorado↗

USGS2006

2005 annual progress report: Elk and bison grazing ecology in the Great Sand Dunes complex of lands

In 2000 the U.S. Congress authorized the expansion of the former Great Sand Dunes National Monument by establishing a new Great Sand Dunes National Park and Preserve in its place, and establishing the Baca National Wildlife Refuge. The establishment of Great Sand Dunes National Park and Preserve and the new Baca National Wildlife Refuge in the San Luis Valley (SLV), Colorado was one of the most significant land conservation actions in the western U.S. in recent years. The action was a result of cooperation between the National Park Service (NPS), U.S. Fish and Wildlife Service (USFWS), Bureau of Land Management (BLM), U.S. Forest Service (USDA-FS), and The Nature Conservancy (TNC). The new national park, when fully implemented, will consist of 107,265 acres, the new national preserve 41,872 acres, and the new national wildlife refuge (USFWS lands) 92,180 acres (fig. 1). The area encompassed by this designation protects a number of natural wonders and features including a unique ecosystem of natural sand dunes, the entire watershed of surface and groundwaters that are necessary to preserve and recharge the dunes and adjacent wetlands, a unique stunted forest, and other valuable riparian vegetation communities that support a host of associated wildlife and bird species. When the National Park was initially established, there were concerns about overconcentrations and impacts on native plant communities of the unhunted segments of a large and possibly growing elk (Cervus elaphus) population. This led to the designation of the Preserve as a compromise solution, where the elk could be harvested. The Preserve Unit, however, will not address all the ungulate management challenges. In order to reduce the current elk population, harvests of elk may need to be aggressive. But aggressive special hunts of elk to achieve population reductions can result in elk avoidance of certain areas or elk seeking refuge in areas where they cannot be hunted, while removals of whole herd segments and abandonment or alterations of migration routes can occur (Smith and Robbins, 1994; Boyce and others, 1991). Elk may seek refuge from hunting in the newly expanded Park Unit and TNC lands where they might overconcentrate and impact unique vegetation communities. In these sites of refugia, or preferred loafing sites, elk and bison could accelerate a decline in woody riparian shrubs and trees. This decline may also be due to changes in hydrology, climatic, or dunal processes, but ungulate herbivory might exacerbate the effects of those processes. To address the questions and needs of local resource managers, a multi-agency research project was initiated in 2005 to study the ecology, forage relations, and habitat relations of elk and bison in the Great Sand Dunes–Sangre de Cristo–Baca complex of lands. Meetings and discussions of what this research should include were started in 2001 with representatives from NPS, USFWS, TNC, the Colorado Division of Wildlife (CDOW), and USDA-FS/BLM. The final study plan was successfully funded in 2004 with research scheduled to start in 2005. The research was designed to encompass three major study elements: (1) animal movements and population dynamics, (2) vegetation and nutrient effects from ungulate herbivory, and (3) development of ecological models, using empirical data collected from the first two components, that will include estimates of elk carrying capacity and management scenarios for resource managers.

Colorado↗

USGS2018

Bipartite networks improve understanding of effects of waterbody size and angling method on angler–fish interactions

Networks used to study interactions could provide insights to fisheries. We compiled data from 27 297 interviews of anglers across waterbodies that ranged in size from 1 to 12 113 ha. Catch rates of fish species among anglers grouped by species targeted generally differed between angling methods (bank or boat). We constructed angler–catch bipartite networks (angling method specific) between anglers and fish and measured several network metrics. There was considerable variation in networks among waterbodies, with multiple metrics influenced by waterbody size. Number of species-targeting angler groups and number of fish species caught increased with increasing waterbody size. Mean number of links for species-targeting angler groups and fish species caught also increased with waterbody size. Connectance (realized proportion of possible links) of angler–catch interaction networks decreased slower for boat anglers than for bank anglers with increasing waterbody size. Network specialization (deviation of number of interactions from expected) was not significantly related to waterbody size or angling methods. Application of bipartite networks in fishery science requires careful interpretation of outputs, especially considering the numerous confounding factors prevalent in recreational fisheries.

Canadian Journal of Fisheries and Aquatic Sciences↗

USGS2001

Assessing ecosystem effects of reservoir operations using food web-energy transfer and water quality models

We investigated the effects on the reservoir food web of a new temperature control device (TCD) on the dam at Shasta Lake, California. We followed a linked modeling approach that used a specialized reservoir water quality model to forecast operation-induced changes in phytoplankton production. A food web–energy transfer model was also applied to propagate predicted changes in phytoplankton up through the food web to the predators and sport fishes of interest. The food web–energy transfer model employed a 10% trophic transfer efficiency through a food web that was mapped using carbon and nitrogen stable isotope analysis. Stable isotope analysis provided an efficient and comprehensive means of estimating the structure of the reservoir's food web with minimal sampling and background data. We used an optimization procedure to estimate the diet proportions of all food web components simultaneously from their isotopic signatures. Some consumers were estimated to be much more sensitive than others to perturbations to phytoplankton supply. The linked modeling approach demonstrated that interdisciplinary efforts enhance the value of information obtained from studies of managed ecosystems. The approach exploited the strengths of engineering and ecological modeling methods to address concerns that neither of the models could have addressed alone: (a) the water quality model could not have addressed quantitatively the possible impacts to fish, and (b) the food web model could not have examined how phytoplankton availability might change due to reservoir operations.

Ecosystems↗

USGS2012

Global exploration and production capacity for platinum-group metals from 1995 through 2015

Platinum-group metals (PGMs) are required in a variety of commercial, industrial, and military applications for many existing and emerging technologies, yet the United States is highly dependent on foreign sources of PGMs. Information on global exploration for PGMs since 1995 has been used in this study as a basis for identifying locations where the industry has determined that exploration has provided data sufficient to warrant development of a new mine or expansion of an existing operation or where a significant increase in capacity for PGMs is anticipated by 2015. Discussions include an overview of the industry and the selected sites, factors affecting mineral supply, and circumstances leading to the development of mineral properties with the potential to affect mineral supply. Of the 52 sites or regional operations that were considered in this analysis, 16 sites were producing before 1995, 28 sites commenced production from 1995 through 2010, and 8 sites were expected to begin production from 2011 through 2015 if development plans came to fruition. The United States imports PGMs primarily from Canada, Russia, South Africa, and Zimbabwe to meet increasing demand for these materials in a variety of specialized and high-tech applications. Feed sources of PGMs are changing in South Africa and Russia, which together accounted for about 89 percent of platinum production and 82 percent of palladium production in 2009. A greater amount of South African PGM capacity is likely to come from deeper, higher cost Upper Group Reef seam 2 deposits and deposits in the Eastern Bushveld area. Future Russian PGM capacity is likely to come from ore zones with generally lower PGM content and different platinum-to-palladium ratios than the nickel-rich ore that dominated PGM supply in the 1990s. Because PGM supply from Canada and Russia is derived as a byproduct of copper and nickel mining, the PGM supply from these countries is influenced by economic, environmental, political, and technological factors affecting exploration for and development of copper and nickel, as well as factors affecting the PGM industry. The recovery of PGMs from mill tailings since 2004 and the recycling of PGMs from catalytic converters, electrical components, and jewelry has increased since 1995 so that recycled PGMs recovered from these products accounted for about 30 percent of the supply of platinum worldwide and 29 percent of the supply of palladium worldwide in 2010. Economic and geopolitical conditions have influenced PGM supply and demand. The global recession of 2008 and 2009 temporarily decreased demand for PGMs and constrained PGM mine exploration and development, at least through 2010. Legislation regulating the structure of the mining sector has affected mining in Russia, South Africa, and Zimbabwe. Stricter vehicle emissions standards in established markets since the 1980s have led to mandatory use of pollution control devices, such as catalytic converters, that contain PGMs and are required on vehicles in expanding markets, such as China and India. It is expected that South Africa, Russia, Canada, and Zimbabwe will continue to be the principal sources of PGM at least for the next decade. Based on this review of the PGM industry, the world’s platinum capacity, expressed in terms of recoverable platinum metal, increased from 1995 through 2010 by 77,000 kilograms (kg) in South Africa, 9,000 kg in Zimbabwe, 6,000 kg in Russia, 2,000 kg in Botswana, and 2,000 kg in Canada. For the same period, palladium capacity worldwide increased by 44,000 kg in South Africa, 22,000 kg in Russia, 8,000 kg in Canada, 8,000 kg in the United States, 7,000 kg in Zimbabwe, and 3,000 kg in Botswana. Platinum capacity worldwide is expected to further increase by 24,000 kg in South Africa, 9,000 kg in Russia, 3,000 kg in Canada, and 2,000 kg in Zimbabwe from 2011 through 2015. Palladium capacity worldwide is likewise expected to increase an additional 16,000 kg in Russia, 14,000 kg in South Africa, 4,000 kg in Zimbabwe, and 1,000 kg in Canada if new or expanded mine and associated processing capacity comes into production as planned. It is likely that the magnitude of these changes in PGM capacity has been influenced by such factors as the global economy, electrical capacity shortages and mine safety concerns in South Africa, and geopolitical conditions in the major PGM producing countries.

Scientific Investigations Report↗

USGS2012

Tools for quantifying isotopic niche space and dietary variation at the individual and population level.

Ecologists are increasingly using stable isotope analysis to inform questions about variation in resource and habitat use from the individual to community level. In this study we investigate data sets from 2 California sea otter ( Enhydra lutris nereis ) populations to illustrate the advantages and potential pitfalls of applying various statistical and quantitative approaches to isotopic data. We have subdivided these tools, or metrics, into 3 categories: IsoSpace metrics, stable isotope mixing models, and DietSpace metrics. IsoSpace metrics are used to quantify the spatial attributes of isotopic data that are typically presented in bivariate (e.g., δ 13 C versus δ 15 N) 2-dimensional space. We review IsoSpace metrics currently in use and present a technique by which uncertainty can be included to calculate the convex hull area of consumers or prey, or both. We then apply a Bayesian-based mixing model to quantify the proportion of potential dietary sources to the diet of each sea otter population and compare this to observational foraging data. Finally, we assess individual dietary specialization by comparing a previously published technique, variance components analysis, to 2 novel DietSpace metrics that are based on mixing model output. As the use of stable isotope analysis in ecology continues to grow, the field will need a set of quantitative tools for assessing isotopic variance at the individual to community level. Along with recent advances in Bayesian-based mixing models, we hope that the IsoSpace and DietSpace metrics described here will provide another set of interpretive tools for ecologists.

Journal of Mammalogy↗

USGS1996

Water quality of the lower Columbia River Basin: Analysis of current and historical water-quality data through 1994

The lower Columbia River Basin includes the river basins draining into the Columbia River below Bonneville Dam—the largest of which is the Willamette River. This report presents the results of a study by the U.S. Geological Survey, done in cooperation with the Lower Columbia River Bi-State Water- Quality Program, to describe the water-quality conditions in the lower Columbia River Basin by interpreting historical data collected and data collected in 1994. Historical water-quality data spanning more than 50 years and comprising more than 200 parameters were collated for interpretation in this report. The U.S. Geological Survey, the Oregon Department of Environmental Quality, and the Washington Department of Ecology collected water-quality data at 10 sites in the lower Columbia River Basin from January to December of 1994. Water-quality constituents measured in 1994 were screened against U.S. Environmental Protection Agency (EPA) and State guidelines. Arsenic, a human carcinogen, was detected in 15 of 16 samples in the lower Columbia River, but was not detected in any of the sampled tributaries. All 15 arsenic detections had concentrations that exceeded both the EPA ambient water-quality criteria for the protection of human health and the EPA human-health advisories for drinking water. Chromium was detected at all four Columbia River sites—most frequently in the Columbia River at Hayden Island. None of the chromium concentrations detected, however, exceeded water-quality criteria or guidelines. Measurements of suspended trace-element concentrations (trace-element concentrations associated with the suspended-sediment fraction) showed that the suspended form is the dominant transport phase for aluminum, iron, and manganese, whereas the dissolved form is the dominant transport phase for arsenic, barium, chromium, and copper. On the basis of tributary loads during summer low-flow months, sources of suspended silver, nickel, aluminum, and antimony exist in the lower Columbia River Basin, whereas the sources of suspended zinc and arsenic exist outside of the lower basin. Twenty organic compounds were detected of the 47 compounds analyzed for this study. None of the organic compounds measured exceeded EPA’s ambient water-quality criteria or drinking-water guidelines. The Willamette River at Portland had the largest number of detections, and all 20 compounds were detected at one time or another at that site. The largest concentrations of the agricultural pesticides, atrazine, metolachlor, and simazine were detected in the Willamette River, where they were detected in 93, 86, 93 percent, respectively, of the samples collected. The highest concentrations of atrazine in the Willamette River were associated with the spring application and fall runoff periods. Both historical and current data showed that the highest water temperatures in the lower Columbia River Basin are present during August. For water years 1977–81 in the Columbia River at Bradwood (river mile 38.9), 75 percent of the daily mean water temperatures during August exceeded 20 degrees Celsius, a “special condition” criterion for the State of Washington. The special condition criterion was exceeded at four sites on the lower Columbia River during July and August, 1994—a period coinciding with season-high air temperatures and low streamflow. Trend tests using data from 1974 to 1994 showed significant (r < 0.05) upward trends for water temperature at the Columbia River at Warrendale and the Willamette River at Portland. Concentrations of dissolved oxygen and total dissolved gas were above saturation levels during high stormflows in the lower Columbia River and the Willamette River during 1994. The high concentrations of total dissolved gas in the Columbia River exceeded Oregon and Washington State standards of 110 percent of saturation and were caused by spilling water at the Columbia River dams. Aquatic life in the lower Columbia River Basin was not subjected to low dissolved-oxygen concentrations. Comparison of dissolved-oxygen concentrations in the Willamette River from 1949–58 to 1972–94 showed a significant increase in dissolved-oxygen concentrations during the low-streamflow months of summer. Trend tests showed significant (r < 0.05) downward trends from 1973 to 1994 for three constituents at the Columbia River at Warrendale: phosphorus in unfiltered water, total dissolved solids, and specific conductance. These trends may be a consequence of more conservative agricultural practices in the area upstream from Warrendale.

Oregon↗

USGS2009

Effects of megascale eruptions on Earth and Mars

Volcanic features are common on geologically active earthlike planets. Megascale or "super" eruptions involving >1000 Gt of magma have occurred on both Earth and Mars in the geologically recent past, introducing prodigious volumes of ash and volcanic gases into the atmosphere. Here we discuss felsic (explosive) and mafi c (flood lava) supereruptions and their potential atmospheric and environmental effects on both planets. On Earth, felsic supereruptions recur on average about every 100-200,000 years and our present knowledge of the 73.5 ka Toba eruption implies that such events can have the potential to be catastrophic to human civilization. A future eruption of this type may require an unprecedented response from humankind to assure the continuation of civilization as we know it. Mafi c supereruptions have resulted in atmospheric injection of volcanic gases (especially SO 2 ) and may have played a part in punctuating the history of life on Earth. The contrast between the more sustained effects of flood basalt eruptions (decades to centuries) and the near-instantaneous effects of large impacts (months to years) is worthy of more detailed study than has been completed to date. Products of mafi c supereruptions, signifi cantly larger than known from the geologic record on Earth, are well preserved on Mars. The volatile emissions from these eruptions most likely had global dispersal, but the effects may not have been outside what Mars endures even in the absence of volcanic eruptions. This is testament to the extreme variability of the current Martian atmosphere: situations that would be considered catastrophic on Earth are the norm on Mars. ?? 2009 The Geological Society of America.

Special Paper of the Geological Society of America↗

USGS2023

Improving ecological data science with workflow management software

Pressing environmental research questions demand the integration of increasingly diverse and large-scale ecological datasets as well as complex analytical methods, which require specialized tools and resources. Computational training for ecological and evolutionary sciences has become more abundant and accessible over the past decade, but tool development has outpaced the availability of specialized training. Most training for scripted analyses focuses on individual analysis steps in one script rather than creating a scripted pipeline, where modular functions comprise an ecosystem of interdependent steps. Although current computational training creates an excellent starting place, linear styles of scripting can risk becoming labor- and time-intensive and less reproducible by often requiring manual execution. Pipelines, however, can be easily automated or tracked by software to increase efficiency and reduce potential errors. Ecology and evolution would benefit from techniques that reduce these risks by managing analytical pipelines in a modular, readily parallelizable format with clear documentation of dependencies. Workflow management software (WMS) can aid in the reproducibility, intelligibility and computational efficiency of complex pipelines. To date, WMS adoption in ecology and evolutionary research has been slow. We discuss the benefits and challenges of implementing WMS and illustrate its use through a case study with the targets r package to further highlight WMS benefits through workflow automation, dependency tracking and improved clarity for reviewers. Although WMS requires familiarity with function-oriented programming and careful planning for more advanced applications and pipeline sharing, investment in training will enable access to the benefits of WMS and impart transferable computing skills that can facilitate ecological and evolutionary data science at large scales.

Methods in Ecology and Evolution↗

USGS2020

Effects of climate change on plague exposure pathways and resulting disease dynamics

Introduction and Objectives: Sylvatic plague, a zoonotic flea-borne disease, caused by the bacterium Yersinia pestis , is relevant to the Department of Defense (DOD), because prairie dogs and other susceptible rodents are present on military installations in several western states. Arthropod-borne diseases, like plague, are thought to be particularly sensitive to local climate conditions. Expected changes in temperature and humidity over the next several decades will likely increase the geographical expansion of plague outbreaks in wildlife. Through a combination of field and laboratory work, along with data-driven modeling, we evaluated the potential effects of climate change on plague exposure pathways in prairie dogs and associated rodents to provide guidance to DOD partners regarding the potential for future outbreaks. Briefly, our specific objectives were to determine the relation between local climate conditions and the prevalence of plague and other pathogens while assessing the ecological roles of specific rodent hosts and vector species in plague dynamics, evaluate flea intensity on rodent hosts and in burrows in relation to local climate conditions, and develop models to predict the effects of climate change on plague dynamics. Technical Approach: Using data and samples collected during a large field study on the effectiveness of vaccination to manage plague in prairie dogs, we assessed rodent/flea assemblages, pathogen prevalence in fleas, and determined how local climate conditions influence flea development rates and relative abundance. Live animals (prairie dogs and some small rodents) were trapped to collect fleas and other samples on 46 prairie dog plots in 6 western states, many sites near DOD lands. At seven additional locations on a latitudinal gradient, fleas were collected from burrows several times per year to assess seasonality and effects of local climate conditions on flea abundance. These data were then used to develop predictive models that could be used to test specific hypotheses. Results: We determined that flea developmental rates, on-host flea abundance, species composition of the flea community, and burrow temperatures varied across a latitudinal gradient. Rodent and flea community composition and abundance differed geographically and were highly specialized. Flea-switching between prairie dogs and short-lived rodents was rare. Flea development rates, on-host flea abundance, and burrow temperatures increased with increasing ambient temperature. Although relative humidity can affect flea development, burrow humidity was uniformly high (~85%) across sampling sites and seasons. A large increase in the number of fleas found on a prairie dog colony, coupled with a greater number of infested burrows, could have substantial effects on plague dynamics in the western United States as the climate warms. In addition to affecting flea load, climate change may also influence body condition of prairie dogs by reducing the amount of forage. This may result in animals being more tolerant of high flea loads (less engaged in grooming behavior) and more vulnerable to disease.

Arizona, Montana, South Dakota, Texas, Utah, Wyomi↗

USGS1978

Comparison of a few recording current meters in San Francisco Bay, CA

A team of research scientists in the U.S. Geological Survey uses San Francisco Bay, California, as an outdoor laboratory to study complicated interactions of physical, chemical, and biological processes which take place in an estuarine environment. A current meter comparison study was conceived because of the need to select a suitable current meter to meet field requirements for current measurements in the Bay. The study took place in south San Francisco Bay, California, in the spring of 1977. An instrument tower which was designed to support instruments free from the conventional mooring line motions was constructed and emplaced in south San Francisco Bay. During a period of two months, four types of recording current meters have been used in the tests. The four types were: (1) Aanderaa, (2) tethered shroud-impeller, (3) drag-inclinometer, and (4) electromagnetic current meters. With the exception of the electromagnetic current meter, one of each type was mounted on the instrument tower, and one of each type was deployed on moorings near the instrument tower. In addition, a wind anemometer and a recording tide gauge were also installed on the tower. This paper discusses the characteristics of each instrument and the accuracy that each instrument can provide when used in an estuarine environment. We pay special attention to our experiences in the field operation with respect to handling of the instruments and to our experiences working up the raw data in the post-deployment data analysis.

California↗

USGS2007

Application of FTLOADDS to Simulate Flow, Salinity, and Surface-Water Stage in the Southern Everglades, Florida

The Comprehensive Everglades Restoration Plan requires numerical modeling to achieve a sufficient understanding of coastal freshwater flows, nutrient sources, and the evaluation of management alternatives to restore the ecosystem of southern Florida. Numerical models include a regional water-management model to represent restoration changes to the hydrology of southern Florida and a hydrodynamic model to represent the southern and western offshore waters. The coastal interface between these two systems, however, has complex surface-water/ground-water and freshwater/saltwater interactions and requires a specialized modeling effort. The Flow and Transport in a Linked Overland/Aquifer Density Dependent System (FTLOADDS) code was developed to represent connected surface- and ground-water systems with variable-density flow. The first use of FTLOADDS is the Southern Inland and Coastal Systems (SICS) application to the southeastern part of the Everglades/Florida Bay coastal region. The need to (1) expand the domain of the numerical modeling into most of Everglades National Park and the western coastal area, and (2) better represent the effect of water-delivery control structures, led to the application of the FTLOADDS code to the Tides and Inflows in the Mangroves of the Everglades (TIME) domain. This application allows the model to address a broader range of hydrologic issues and incorporate new code modifications. The surface-water hydrology is of primary interest to water managers, and is the main focus of this study. The coupling to ground water, however, was necessary to accurately represent leakage exchange between the surface water and ground water, which transfers substantial volumes of water and salt. Initial calibration and analysis of the TIME application produced simulated results that compare well statistically with field-measured values. A comparison of TIME simulation results to previous SICS results shows improved capabilities, particularly in the representation of coastal flows. This improvement most likely is due to a more stable numerical representation of the coastal creek outlets. Sensitivity analyses were performed by varying frictional resistance, leakage, barriers to flow, and topography. Changing frictional resistance values in inland areas was shown to improve water-level representation locally, but to have a negligible effect on area-wide values. These changes have only local effects and are not physically based (as are the unchanged values), and thus have limited validity. Sensitivity tests indicate that the overall accuracy of the simulation is diminished if leakage between surface water and ground water is not simulated. The inclusion of a major road as a complete barrier to surface-water flow influenced the local distribution and timing of flow; however, the changes in total flow and individual creekflows were negligible. The model land-surface altitude was lowered by 0.1 meter to determine the sensitivity to topographic variation. This topographic sensitivity test produced mixed results in matching field data. Overall, the representation of stage did not improve definitively. A final calibration utilized the results of the sensitivity analysis to refine the TIME application. To accomplish this calibration, the friction coefficient was reduced at the northern boundary inflow and increased in the southwestern corner of the model, the evapotranspiration function was varied, additional data were used for the ground-water head boundary along the southeast, and the frictional resistance of the primary coastal creek outlet was increased. The calibration improved the match between measured and simulated total flows to Florida Bay and coastal salinities. Agreement also was improved at most of the water-level sites throughout the model domain.

Scientific Investigations Report↗

USGS2022

Annotated bibliography of scientific research on pygmy rabbits published from 1990 to 2020

Integrating recent scientific knowledge into management decisions supports effective natural resource management and can lead to better resource outcomes. However, finding and accessing scientific knowledge can be time consuming and costly. To assist in this process, the U.S. Geological Survey (USGS) is creating a series of annotated bibliographies on topics of management concern for western lands. Previously published reports introduced a methodology for preparing annotated bibliographies to facilitate the integration of recent, peer-reviewed science into resource management decisions. Therefore, relevant text from those efforts is reproduced here to frame the presentation. Sagebrush ecosystems throughout North America face management challenges including habitat loss and fragmentation. Brachylagus idahoensis (pygmy rabbits) are a sagebrush-obligate species that has experienced population declines and range contraction in recent decades. A disjunct population of pygmy rabbits in the Columbia Basin in Washington was listed as federally endangered in 2003. Due to their specialized habitat requirements and low dispersal ability, pygmy rabbits are a high priority for managers throughout their range. We compiled and summarized peer-reviewed journal articles, data products, and formal technical reports (such as U.S. Forest Service General Technical Reports and U.S. Geological Survey Open-File Reports) on pygmy rabbits published between January 1, 1990 and December 31, 2020. We first conducted a structured search of three reference databases and three government databases using the phrase “pygmy rabbit” or “ Brachylagus idahoensis .” We refined the initial list of products by removing (1) duplicates, (2) products not written in English, (3) publications that were not focused on North America, (4) publications that were not published as research, data products, or scientific review articles in peer-reviewed journals or as formal technical reports, and (5) products for which pygmy rabbits were not a research focus or for which the study did not present new data or findings about pygmy rabbits. We summarized each product using a consistent structure (background, objectives, methods, location, findings, and implications) and identified the management topics (for example, captive breeding, habitat characteristics, and population estimates) addressed by each product. We also noted which publications included new publicly available geospatial data. The review process for this annotated bibliography included an initial internal colleague review of each summary, requesting input on each summary from an author of the original publication, and a formal peer review. Our initial searches resulted in 2,285 total products, of which 105 met our criteria for inclusion. Sensitive/rare wildlife, behavior or demographics, site-scale habitat characteristics, habitat selection, and effects distances or spatial scale were the management topics most commonly addressed. The online version of this bibliography, Science for Resource Managers, will be searchable by topic, location, and year; it will include links to each original publication, where available. The studies compiled and summarized here may inform planning and management actions that seek to maintain and restore sagebrush landscapes and associated native species across the western United States.

Open-File Report↗

USGS1999

Evaluation of the effectiveness of an urban stormwater treatment unit in Madison, Wisconsin, 1996-97

An urban stormwater treatment unit was tested as part of an ongoing program of urban nonpoint- pollution research in Madison, Wis. Flow measurements were made and water samples were collected at the inlet to, outlet from, and bypass around the treatment chamber of the device that was installed to collect the runoff from a city maintenance yard. About 90 percent of the runoff water from the 4.3-acre basin was treated by the unit. The remaining 10 percent bypassed the treatment chamber when the flow rate reached approximately 500 gallons per minute. A 24-percent difference between the estimated amount (405 kilograms) and the actual amount (536 kilograms) of retained material in the treatment chamber may be attributed to bedload material that the automatic samplers could not effectively collect. Assuming this, 8 percent of the total mass in the untreated runoff water was estimated as the unsampled bedload. On the basis of water-sample data collected over the course of the study, the suspended solids removal efficiency of treatment chamber was about 25 percent, and the efficiency of the unit as a whole was 21 percent. If the unsampled bedload material was accounted for, the treatment-chamber efficiency was 33 percent. About 19 percent of the total phosphorus was removed from the water that passed through the treatment chamber and 17 percent was removed by the unit as a whole. Total polycyclic aromatic hydrocarbon (PAH) loads were reduced about 39 percent by the treatment chamber and 34 percent by the unit as a whole; these were some of the most effectively removed constituents. Total metals were reduced about 20 to 30 percent by both the treatment chamber and the unit as a whole. In general, dissolved constituents were unaffected by the unit. The material retained in the treatment chamber had high concentrations of lead and PAH and may be subject to special disposal restrictions based on those concentrations and the presence of benzo(a)anthracene. The chemical makeup of the retained material in other similar stormwater treatment units will probably vary depending on the land use and activities in the drainage basin.

Wisconsin↗

USGS2016

Analysis of hydrologic and geochemical time-series data at James Cave, Virginia: Implications for epikarst influence on recharge in Appalachian karst aquifers

The epikarst, which consists of highly weathered rock in the upper vadose zone of exposed karst systems, plays a critical role in determining the hydrologic and geochemical characteristics of recharge to an underlying karst aquifer. This study utilized time series (2007–2014) of hydrologic and geochemical data of drip water collected within James Cave, Virginia, to examine the influence of epikarst on the quantity and quality of recharge in a mature, doline-dominated karst terrain. Results show a strong seasonality of both hydrology and geochemistry of recharge, which has implications for management of karst aquifers in temperate climatic zones. First, recharge (discharge from the epikarst to the underlying aquifer) reaches a maximum between late winter and early spring, with the onset of the recharge season ranging from as early as December to as late as March during the study period. The timing and duration of the recharge season were found to be a function of precipitation in excess of evapotranspiration on a seasonal time scale. Secondly, seasonally variable residence times for water in the epikarst influence rock-water interaction and, hence, the geochemical characteristics of recharge. Overall, results highlight the strong and complex influence that the epikarst has on karst recharge, which requires long-term and high-resolution data sets to accurately understand and quantify.

Virginia↗

USGS1973

High survival and homing rate of hand-reared wild-strain mallards

In the summer of 1970, 648 (329 males and 319 females) hand-reared wild-strain mallards ( Anas platyrhynchos ) were banded and released at the Arrowwood National Wildlife Refuge, Edmunds, North Dakota. The females were also marked with numbered nasal saddles. Liberation was by the gentle release method, and no special effort was made to isolate or condition the ducklings prior to release. Ducklings were placed in an enclosed pond area at 25 to 45 days of age. Altogether, 627 (97 percent) ducklings reached flight age and dispersed gradually into the wild. All had left the release area by 25 November. First-year band recovery reports indicated that 68 (11 percent) of the birds were shot in 15 states. Their migration pattern was similar to that for immature wild mallards banded in North Dakota in 1970. Eighty-nine (33 percent) of a possible 270 marked females returned to Arrowwood Refuge during 1971. When consideration is given to assumed normal natural mortality and crippling loss, an estimated minimum of 43 percent of the surviving females returned to the release area. Returning birds not observed would raise this figure even higher. This potential homing rate is considerably higher than rates reported for other studies using various strains of mallards. Numerous observations of nests and broods indicated that breeding behavior and nesting success were similar to those of wild mallards in the area. The success of this release is attributed to the inherent capability of hand-reared, wild-strain mallards to revert to their wild behavior, and to the high survival to flight age and first fall migration afforded by the gentle release in a sanctuary area. Indications are that releases of this type under the described conditions can be used to increase the breeding population of mallards in a local area.

North Dakota↗

USGS1982

Determination and analysis of bearing capacity of calcarenites off the Florida Keys

A specially designed instrument was used to determine the in situ bearing capacity at 12 sites in the carbonate sand seaward of the Florida Keys. The resulting data set not only represents unique information in such an environment, but also provided an opportunity to determine whether bearing capacity is controlled by any specific property of the calcarenites, or, conversely, whether the bearing-capacity value could be used as an index of a particular substrate characteristic. The in sltu measurements were made in several subenvironments in order to bracket the variability of sediment properties throughout the area. Samples were collected at each bearing-capacity test site and w .ere analyzed for selected geological and geotechnical properties, including texture, grain shapes, and biological constituents. No relationship was found between bearing capacity and any of the analyzed properties of the sediment. Although many salient characteristics of calcarenites exist, at the stress levels used in this study their influence is either masked owing to the complex interaction of properties that leads to a specific bearing-capacity value or, at least in these sediments, is absent.

Open-File Report↗