Digital Commons Network^™

The Geologic Records Of Dust In The Quaternary, Daniel R. Muhs

United States Geological Survey: Staff Publications

Study of geologic records of dust composition, sources and deposition rates is important for understanding the role of dust in the overall planetary radiation balance, fertilization of organisms in the world’s oceans, nutrient additions to the terrestrial biosphere and soils, and for paleoclimatic reconstructions. Both glacial and non-glacial processes produce fine-grained particles that can be transported by the wind. Geologic records of dust flux occur in a number of depositional archives for sediments: (1) loess deposits; (2) lake sediments; (3) soils; (4) deep-ocean basins; and (5) ice sheets and smaller glaciers. These archives have several characteristics that make them highly …

Effects Of Linking A Soil-Water-Balance Model With A Groundwater-Flow Model, Jennifer S. Stanton, Derek W. Ryter, Steven M. Peterson

United States Geological Survey: Staff Publications

A previously published regional groundwater-flow model in north-central Nebraska was sequentially linked with the recently developed soil-water-balance (SWB) model to analyze effects to groundwater-flow model parameters and calibration results. The linked models provided a more detailed spatial and temporal distribution of simulated recharge based on hydrologic processes, improvement of simulated groundwater-level changes and base flows at specific sites in agricultural areas, and a physically based assessment of the relative magnitude of recharge for grassland, nonirrigated cropland, and irrigated cropland areas. Root-mean-squared (RMS) differences between the simulated and estimated or measured target values for the previously published model and linked models …

Hawaiian Forest Birds: The Past, Present And Future Status Of An Endangered Avifauna, Dennis A. Lapointe, Carter T. Atkinson, Paul C. Banko, Richard J. Camp, P. Marcos Gorresen, James D. Jacobi, Thane K. Pratt, Michael D. Samuel

United States Geological Survey: Staff Publications

The Hawaiian forest birds are among the most endangered avifauna of the world. Entire bird groups have disappeared from the Hawaiian Islands, and of the more than fifty, historically-known species of Hawaiian honeycreeper, only 17 remain. Due to the extreme geographical isolation, few birds colonized the Hawaiian Islands but, released from direct competition, predation, and disease, these founders flourished and evolved amid the heterogeneous geography of the archipelago. This process of colonization and speciation is best characterized by the honeycreepers; the largest radiation of endemic forest birds in the Hawaiian Islands, or for that matter, birds on any oceanic archipelago. …

Chapter 4 Management Of Wetlands For Wildlife, Matthew J. Gray, Heath M. Hagy, J. Andrew Nyman, Joshua D. Stafford

United States Geological Survey: Staff Publications

Wetlands are highly productive ecosystems that provide habitat for a diversity of wildlife species and afford various ecosystem services. Managing wetlands effectively requires an understanding of basic ecosystem processes, animal and plant life history strategies, and principles of wildlife management. Management techniques that are used differ depending on target species, coastal versus interior wetlands, and available infrastructure, resources, and management objectives. Ideally, wetlands are managed as a complex, with many successional stages and hydroperiods represented in close proximity. Managing wetland wildlife typically involves manipulating water levels and vegetation in the wetland, and providing an upland buffer. Commonly, levees and water …

Ice-Age Megafauna In Arctic Alaska: Extinction, Invasion, Survival, Daniel H. Mann, Pamela Groves, Michael L. Kunz, Richard E. Reanier, Benjamin V. Gaglioti

United States Geological Survey: Staff Publications

Radical restructuring of the terrestrial, large mammal fauna living in arctic Alaska occurred between 14,000 and 10,000 years ago at the end of the last ice age. Steppe bison, horse, and woolly mammoth became extinct, moose and humans invaded, while muskox and caribou persisted. The ice age mega fauna was more diverse in species and possibly contained 6x more individual animals than live in the region today. Mega faunal biomass during the last ice age may have been 30x greater than present. Horse was the dominant species in terms of number of individuals. Lions, short-faced bears, wolves, and possibly grizzly …

Origin Of The Sinai-Negev Erg, Egypt And Israel: Mineralogical And Geochemical Evidence For The Importance Of The Nile And Sea Level History, Daniel R. Muhs, Joel Roskin, Haim Tsoar, Gary Skipp, James Budahn, Amihai Sneh, Naomi Porat, Jean-Daniel Stanley, Itzhak Katra, Dan G. Blumberg

United States Geological Survey: Staff Publications

The Sinai-Negev erg occupies an area of 13,000 km² in the deserts of Egypt and Israel. Aeolian sand of this erg has been proposed to be derived from the Nile Delta, but empirical data supporting this view are lacking. An alternative source sediment is sand from the large Wadi El Arish drainage system in central and northern Sinai. Mineralogy of the Negev and Sinai dunes shows that they are high in quartz, with much smaller amounts of K-feldspar and plagioclase. Both Nile Delta sands and Sinai wadi sands, upstream of the dunes, also have high amounts of quartz relative …

Chronology And Provenance Of Last-Glacial (Peoria) Loess In Western Iowa And Paleoclimatic Implications, Daniel R. Muhs, E. Arthur Bettis Iii, Helen M. Roberts, Stephen S. Harlan, James B. Paces, Richard L. Reynolds

United States Geological Survey: Staff Publications

Geologic archives show that the Earth was dustier during the last glacial period. One model suggests that increased gustiness (stronger, more frequent winds) enhanced dustiness. We tested this at Loveland, Iowa, one of the thickest deposits of last-glacial-age (Peoria) loess in the world. Based on K/Rb and Ba/Rb, loess was derived not only from glaciogenic sources of the Missouri River, but also distal loess from non-glacial sources in Nebraska. Optically stimulated luminescence (OSL) ages provide the first detailed chronology of Peoria Loess at Loveland. Deposition began after ~27 ka and continued until ~17 ka. OSL ages also indicate that mass …

A Global Standard For Monitoring Coastal Wetland Vulnerability To Accelerated Sea-Level Rise, Edward L. Webb, Daniel A. Friess, Ken W. Krauss, Donald R. Cahoon, Glenn R. Guntenspergen, Jacob Phelps

United States Geological Survey: Staff Publications

Sea-level rise threatens coastal salt-marshes and mangrove forests around the world, and a key determinant of coastal wetland vulnerability is whether its surface elevation can keep pace with rising sea level. Globally, a large data gap exists because wetland surface and shallow subsurface processes remain unaccounted for by traditional vulnerability assessments using tide gauges. Moreover, those processes vary substantially across wetlands, so modelling platforms require relevant local data. The low-cost, simple, high-precision rod surface-elevation table–marker horizon (RSET-MH) method fills this critical data gap, can be paired with spatial data sets and modelling and is financially and technically accessible to every …

Carbon Storage And Sequestration By Trees In Urban And Community Areas Of The United States, David J. Nowak, Eric J. Greenfield, Robert E. Hoehn, Elizabeth Lapoint

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Carbon storage and sequestration by urban trees in the United States was quantified to assess the magnitude and role of urban forests in relation to climate change. Urban tree field data from 28 cities and 6 states were used to determine the average carbon density per unit of tree cover. These data were applied to statewide urban tree cover measurements to determine total urban forest carbon storage and annual sequestration by state and nationally. Urban whole tree carbon storage densities average 7.69 kg C m^‒2 of tree cover and sequestration densities average 0.28 kg C m^‒2 of tree …

Climatic Niche, Ecological Genetics, And Impact Of Climate Change On Eastern White Pine (Pinus Strobus L.): Guidelines For Land Managers, Dennis G. Joyce, Gerald E. Rehfeldt

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

Approximately, 123,500 forest inventory and ecological ground plots representing eastern North America were used to predict the contemporary distribution of eastern white pine (Pinus strobus L.) from climate. The random forests classification tree procedures produced an 8-variable algorithm that had an 8% overall error rate. Erroneous predictions of presence, or errors of commission, were 13%, while falsely predicting absence, or errors of omission were 1%. Climate-based multiple regression models were developed to describe patterns of genetic variation among 112 populations representing the range of P. strobus in Ontario, Canada east of Lake Superior. Degree days >5°C was the best …

Modeling Harvest And Biomass Removal Effects On The Forest Carbon Balance Of The Midwest, Usa, Scott D. Peckham, Stith T. Gower, Charles H. Perry, Barry T. Wilson, Kirk M. Stueve

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

The objective of this study was to use an ecosystem process model, Biome-BGC, to explore the effects of different harvest scenarios on major components of the carbon budget of 205,000 km² of temperate forest in the Upper Midwest region of the U.S. We simulated seven harvest scenarios varying the (i) amount of harvest residue retained, (ii) total harvest area, and (iii) harvest type (clear-cut and selective) to assess the potential impacts on net biome production (NBP), net primary production (NPP), and total vegetation carbon. NBP was positive (C sink) in year 1 (2004) and generally decreased over the 50-year …

Small Geographic Range But Not Panmictic: How Forests Structure The Endangered Point Arena Mountain Beaver (Aplodontia Rufa Nigra), William J. Zielinski, Fredrick V. Schlexer, Sean A. Parks, Kristine L. Pilgrim, Michael K. Schwartz

United States Department of Agriculture, Forest Service / University of Nebraska-Lincoln: Faculty Publications

The landscape genetics framework is typically applied to broad regions that occupy only small portions of a species’ range. Rarely is the entire range of a taxon the subject of study. We examined the landscape genetic structure of the endangered Point Arena mountain beaver (Aplodontia rufa nigra), whose isolated geographic range is found in a restricted (85 km²) but heterogenous region in California. Based on its diminutive range we may predict widespread gene flow and a relatively weak role for landscape variation in defining genetic structure. We used skin, bone, tissue and noninvasively collected hair samples …

Avian Mortality At Communication Towers In The United States And Canada: Which Species, How Many, And Where?, Travis Longcore, Catherine Rich, Pierre Mineau, Beau Macdonald, Daniel G. Bert, Lauren M. Sullivan, Erin Mutrie, Sidney A. Gauthreaux Jr., Michael L. Avery, Robert L. Crawford, Albert M. Manville Ii, Emilie R. Travis, David Drake

United States Department of Agriculture Wildlife Services: Staff Publications

Birds migrating to and from breeding grounds in the United States and Canada are killed by the millions in collisions with lighted towers and their guy wires. Avian mortality at towers is highly variable across species, and the importance to each population depends on its size and trajectory. Building on our previous estimate of avian mortality at communication towers, we calculated mortality by species and by regions. To do this, we constructed a database of mortality by species at towers from available records and calculated the mean proportion of each species killed at towers within aggregated Bird Conservation Regions. These …

Use Of Dairies By Postreproductive Flocks Of European Starlings, H. Jeffrey Homan, Jeffrey T. Lejeune, D. L. Pearl, T. W. Seamans, Thomas W. Seamans, A.A. Slowik, Mark R. Morasch, George M. Linz

United States Department of Agriculture Wildlife Services: Staff Publications

Knowledge of the behavior and movement patterns of European starlings (Sturnus vulgaris L.) is important to wildlife managers that seek to resolve conflicts at livestock facilities. We captured and radio tagged 10 starlings at each of 5 dairies in northeastern Ohio. From September 19 to October 31, 2007, we obtained sufficient data from 40 birds to study their behavior and movements. The birds visited the dairies where they were initially captured (home sites) on 85% of the days, spending 58% of each day at the dairies. Onsite arrival and departure times were 2.5 h after sunrise and 3.1 h …

Stream Hierarchy Defines Riverscape Genetics Of A North American Desert Fish, Matthew W. Hopken, Marlis R. Douglas, Michael E. Douglas

United States Department of Agriculture Wildlife Services: Staff Publications

Global climate change is apparent within the Arctic and the south-western deserts of North America, with record drought in the latter reflected within 640 000 km2 of the Colorado River Basin. To discern the manner by which natural and anthropogenic drivers have compressed Basin-wide fish biodiversity, and to establish a baseline for future climate effects, the Stream Hierarchy Model (SHM) was employed to juxtapose fluvial topography against molecular diversities of 1092 Bluehead Sucker (Catostomus discobolus). MtDNA revealed three geomorphically defined evolutionarily significant units (ESUs): Bonneville Basin, upper Little Colorado River and the remaining Colorado River Basin. Microsatellite analyses …

Seroprevalence Of Brucellosis In Livestock Within Three Endemic Regions Of The Country Of Georgia, Eliso Mamisashvili, Ian T. Kracalik, Tinatin Onashvili, Lela Kerdzevadze, Ketevan Goginashvili, Tamar Tigilauri, Marina Donduashvili, Marina Nikolaishvili, Irma Beradze, Marina Zakareishvili, Maka Kokhreidze, Makvala Gelashvili, Nino Vepkhvadze, S. Elizabeth Rácz, Philip H. Elzer, Mikeljon P. Nikolich, Jason K. Blackburn

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Brucellosis is the one of most common livestock zoonoses in Georgia, resulting in significant economic losses. Livestock were sampled in three regions of Georgia (Kakheti, Kvemo Kartli, Imereti). Districts that historically reported high numbers of brucellosis related morbidity were selected for serological, bacteriological and molecular surveys. Surveying efforts yielded samples from 10,819 large and small ruminants. In total, 735 serological tests were positive on Rose Bengal and 33 bacterial isolates were recovered and identified as Brucella melitensis or Brucella abortus by microbiology and AMOS-PCR. A Bayesian framework was implemented to estimate the true prevalence of the disease given an imperfect …

On The Morphology And Taxonomy Of Griphobilharzia Amoena Platt And Blair, 1991 (Schistosomatoidea), A Dioecious Digenetic Trematode Parasite Of The Freshwater Crocodile, Crocodylus Johnstoni, In Australia [Critical Comment], Thomas R. Platt, Eric P. Hoberg, Leslie A. Chisholm

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Griphobilharzia amoena Platt and Blair, 1991 was originally described was originally described as a dioecious trematode, parasitic in the circulatory system of the Australian freshwater crocodile, Crocodylus johnstoni, with the female completely enclosed in a gynecophoric chamber of the male and the two worms orientated anti-parallel to each other. A recent publication questions the original description, arguing that G. amoena is monoecious and, as a consequence, the species was transferred to Vasotrema Stunkard, 1928 (Spirorchiidae) as Vasotrema amoena n. comb. We provide photomicrographic evidence that the original description of G. amoena is correct and that Griphobilharzia Platt and Blair, …

Fostering Climate Change Education In The Central Great Plains: A Public Engagement Approach, Lisa M. Pytlikzillig, Timothy Steffensmeier, Amber Campbell Hibbs, Ben Champion, Eric Hunt, John A. Harrington, Jr., Jacqueline D. Spears, Natalie Umphlett, Tarik Abdel-Monem, Roger Bruning, Daniel Kahl

Lisa PytlikZillig Publications

Despite its increasing importance for sustainability, building widespread competency in the basic principles of climate literacy among the United States general public is a great challenge. This article describes the methods and results of a public engagement approach to planning climate change education in the Central Great Plains of the United States. Our approach incorporated contextual and lay expertise approaches to public engagement with a focus on supporting the self-determination of the specific stakeholder groups–rural producers, educators, and community members. An integration of results from the focus groups reveal that our approach was received positively and elicited a number of …

The Relative Influences Of Climate And Catchment Processes On Holocene Lake Development In Glaciated Regions, Sherilyn C. Fritz, N. J. Anderson

Department of Earth and Atmospheric Sciences: Faculty Publications

Following deglaciation, the long-term pattern of change in diatom communities and the inferred history of the aquatic environment are affected by a hierarchy of environmental controls. These include direct climate impacts on a lake’s thermal and hydrologic budgets, aswell as the indirect affects of climate on catchment processes, such as weathering, soil development, microbial activity, fire, and vegetation composition and productivity,which affect the transfer of solutes and particulates from the terrestrial ecosystem into the lake. Some of these catchment influences on lacustrine systems operate as time-dependent patterns of primary succession that are set in motion by glacier retreat. This paper …

Bacillus Thuringiensis: Transgenic Crops, Julie A. Peterson, John J. Obrycki, James D. Harwood

Department of Entomology: Faculty Publications

Bacillus thuringiensis (Bt) crops, genetically modified to express insecticidal toxins that target key pests of corn, cotton, rice, potato, and other crops, have been rapidly adopted and have become dominant fixtures in agroecosystems throughout the world. Due to the constitutive nature of Bt toxin expression, insecticidal proteins may be found in nearly all plant tissues, presenting multiple sources for Bt toxins to enter the environment, thus creating complex direct and indirect pathways for non-target organisms to be exposed to insecticidal proteins. The environmental impacts of Bt crops have been widely debated, although both benefits and risks do exist. Benefits of …

A Comparison Of Bats And Rodents As Reservoirs Of Zoonotic Viruses: Are Bats Special?, Angela D. Luis, David T. S. Hayman, Thomas J. O'Shea, Paul M. Cryan, Amy T. Gilbert, Juliet R. C. Pulliam, James N. Mills, Mary E. Timonin, Craig K. R. Willis, Andrew A. Cunningham, Anthony R. Fooks, Charles E. Rupprecht, James L. N. Wood, Colleen T. Webb

United States Department of Agriculture Wildlife Services: Staff Publications

Bats are the natural reservoirs of a number of high-impact viral zoonoses. We present a quantitative analysis to address the hypothesis that bats are unique in their propensity to host zoonotic viruses based on a comparisonwith rodents, another important host order. We found that bats indeed host more zoonotic viruses per species than rodents, and we identified life-history and ecological factors that promote zoonotic viral richness. More zoonotic viruses are hosted by species whose distributions overlap with a greater number of other species in the same taxonomic order (sympatry). Specifically in bats, therewas evidence for increased zoonotic viral richness in …

On The Edge: A Genetic Assessment Of Aplodontia Rufa From The Edge Of Their Distribution, Antoinette J. Piaggio, Jennifer Jeffers

United States Department of Agriculture Wildlife Services: Staff Publications

Aplodontia rufa (mountain beaver) is considered the sole remaining extant genus and species of an ancient lineage that once broadly inhabited the Great Basin and is now restricted to the Pacific Northwest and portions of California and Nevada. Aplodontia rufa californica in Nevada is distributed patchily at the edge of mountain beaver distribution. Due to concern over the status of these populations this subspecies is listed in Nevada as sensitive. The Nevada Department of Wildlife is concerned about the status of Aplodontia rufa californica populations scattered across areas of central western Nevada and has worked to gain an understanding of …

The R Journal (December 2012) 4(2): Complete Issue, The R Foundation

The R Journal

Contributing Articles

What's in a Name? Paul Murrell

It's Not What You Draw, It's What You Don't Draw, Paul Murrell

Debugging grid Graphics, Paul Murrell and Velvet Ly

frailtyHL: A Package for Fitting Frailty Models with H-likelihood, Il Do Ha, Maengseok Noh, and Youngjo Lee

influence.ME: Tools for Detecting Influential Data in Mixed Effects Models, Rense Nieuwenhuis, Manfred te Grotenhuis and Ben Pelzer

The crs Package: Nonparametric Regression Splines for Continuous and Categorical Predictors, Zhenghua Nie and Jeffrey S. Racine

Rfit: Rank-based Estimation for Linear Models, John D. Kloke and Joseph W. McKean

Graphical Markov Models with Mixed Graphs in …

It's Not What You Draw, It's What You Don't Draw, Paul Murrell

The R Journal

The R graphics engine has new support for drawing complex paths via the functions polypath() and grid.path(). This article explains what is meant by a complex path and demonstrates the usefulness of complex paths in drawing non-trivial shapes, logos, customised data symbols, and maps.

Plant Community Composition And Structure Monitoring For Scotts Bluff National Monument, 2012 Annual Report, Isabel W. Ashton, Michael Prowatzke, Stephen K. Wilson

United States National Park Service: Publications

Executive Summary

the last remnants of native mixed-grass prairie in the region. The Northern Great Plains Inventory & Monitoring Network (NGPN) surveyed 8 long-term monitoring plots in Scotts Bluff National Monument in 2012 as part of an effort to better understand the condition of plant communities in the park. We measured plant diversity and cover, estimated tree and shrub density, looked for the presence of exotic species that are of concern to park management, and evaluated the amount of human and natural disturbance at all plots. This effort was the second year in a multiple-year venture to document the current …

Connecting Children To Nature: A Multiple Case Study Of Nature Center Preschools, Patti Ensel Bailie

Department of Teaching, Learning, and Teacher Education: Theses and Other Student Research

Environmental degradation, childhood obesity, and aggression of youth are societal problems that appear unconnected. However, their cause (and possible solution) may be linked to a common experience – the amount and quality of time spent in the natural world. Environment based education, significant life experience research, and studies involving urban youth and green spaces have shown that children’s experiences in the natural world have a positive effect on their attitudes, behaviors, and environmental awareness. Nature center based preschools are one approach for connecting children and nature, but little is known about the quality and consistency of their practices. This study …

Which Study Method Works Best? A Comparison Of Soar And Sq3r For Text Learning, Sarah C. Kasson

College of Education and Human Sciences: Dissertations, Theses, and Student Research

One hundred thirty-eight college students participated in a study comparing the SOAR (Select, Organize, Association, Regulate) and SQ3R (Survey, Question, Read, Recite, Review) study systems to each other and to students’ preferred study methods. Though both systems have been researched independently, just one other study has compared these study systems to each other. College students were assigned randomly to one cell of a 2x2 factorial design (method: SOAR or SQ3R; material: supplement or no supplement) or to a preferred-study-method control group. Groups were trained in their respective system (SOAR, SQ3R, or control) and then given materials about educational measurement to …

Evaluation Of The Environmental Impacts Of Bridge Deck Runoff, Shannon L. Bartelt-Hunt, Lauren Swadener, Ekizabeth G. Jones

Nebraska Department of Transportation: Research Reports

Bridges are located in very close proximity to receiving waters, and regulatory agencies often require specific stormwater control measures for bridge deck runoff. While there is some information available on roadway runoff, few studies have focused on bridge deck runoff. Currently, there is no information available regarding the impacts of bridge deck runoff on receiving waters in Nebraska. Due to the cost, maintenance, and design issues associated with implementing structural controls for bridge deck runoff, it is important to develop a better understanding of the relationship between bridge deck runoff and potential impacts to receiving streams. The objectives of this …

Fish Assemblage Structure In Black Hills, South Dakota Streams, Luke D. Schultz, Sarah J. Lewis, Katie Nicole Bertrand

The Prairie Naturalist

Understanding factors structuring fish assemblages in a particular area is valuable to both sport fishery management and native species conservation. Fish assemblages in the Black Hills are unique to South Dakota because they contain economically valuable introduced salmonids as well as native species of conservation need. Our objective was to examine the relationship between fish assemblages and geomorphic and reach-scale habitat features across multiple stream reaches in the Black Hills. Canonical correspondence analysis, a direct gradient ordination analysis, indicated that factors operating at multiple spatial scales interacted to structure fish assemblages. There also was indication of segregation between native species …

Insights From Characterizing Extinct Human Gut Microbiomes, Raul Y. Tito, Dan Knights, Jessica Metcalf, Alexandra J. Obregon-Tito, Lauren Cleeland, Fares Najar, Bruce Roe, Karl Reinhard, Kristin Sobolik, Samuel Belknap, Morris Foster, Paul Spicer, Rob Knight, Cecil M. Lewis, Jr.

School of Natural Resources: Faculty Publications

In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (~8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to …