Determining the 95% limit of detection for waterborne pathogen analyses from primary concentration to qPCR
Joel P. Stokdyk, Aaron D. Firnstahl, Susan K. Spencer, Tucker R Burch, Mark A. Borchardt
2016, Water Research (96) 105-113
The limit of detection (LOD) for qPCR-based analyses is not consistently defined or determined in studies on waterborne pathogens. Moreover, the LODs reported often reflect the qPCR assay alone rather than the entire sample process. Our objective was to develop an approach to determine the 95% LOD (lowest concentration at...
Tarangire revisited: Consequences of declining connectivity in a tropical ungulate population
Thomas A. Morrison, William A. Link, William D. Newmark, Charles A.H. Foley, Douglas T. Bolger
2016, Biological Conservation (197) 53-60
The hyper-abundance of migratory wildlife in many ecosystems depends on maintaining access to seasonally available resources. In Eastern and Southern Africa, land-use change and a loss of connectivity have coincided with widespread declines in the abundance and geographic range of ungulate populations. Using photographic capture-mark-recapture, we examine the historical pattern...
Desert tortoise annotated bibliography, 1991-2015
Kristin H. Berry, Lisa M. Lyren, Jeremy S. Mack, L. Arriana Brand, Dustin A. Wood
2016, Open-File Report 2016-1023
Introduction Agassiz’s desert tortoise, Gopherus agassizii, was considered a single species for 150 years after its discovery by James Cooper (1861), with a geographic range extending from southeastern California, southern Nevada, and southwestern Utah southward into northern Sinaloa, Mexico (Murphy and others, 2011). What was once G. agassizii is now...
Establishing a pre-mining geochemical baseline at a uranium mine near Grand Canyon National Park, USA
David L. Naftz, Katherine Walton-Day
2016, Geoderma (7) 76-92
During 2012, approximately 404,000 ha of Federal Land in northern Arizona was withdrawn from consideration of mineral extraction for a 20-year period to protect the Grand Canyon watershed from potentially adverse effects of U mineral exploration and development. The development, operation, and reclamation of the Canyon Mine during the withdrawal...
Optimized methods for total nucleic acid extraction and quantification of the bat white-nose syndrome fungus, Pseudogymnoascus destructans, from swab and environmental samples
Michelle Verant, Elizabeth A. Bohuski, Jeffrey M. Lorch, David S. Blehert
2016, Journal of Veterinary Diagnostic Investigation (28) 110-118
The continued spread of white-nose syndrome and its impacts on hibernating bat populations across North America has prompted nationwide surveillance efforts and the need for high-throughput, noninvasive diagnostic tools. Quantitative real-time polymerase chain reaction (qPCR) analysis has been increasingly used for detection of the causative fungus, Pseudogymnoascus destructans, in both bat-...
Available data support protection of the Southwestern Willow Flycatcher under the Endangered Species Act
Tad C. Theimer, Aaron D. Smith, Sean M. Mahoney, Kirsten E. Ironside
2016, The Condor (118) 289-299
Zink (2015) argued there was no evidence for genetic, morphological, or ecological differentiation between the federally endangered Southwestern Willow Flycatcher (Empidonax traillii extimus) and other Willow Flycatcher subspecies. Using the same data, we show there is a step-cline in both the frequency of a mtDNA haplotype and in plumage variation roughly...
Habitat use and foraging patterns of molting male Long-tailed Ducks in lagoons of the central Beaufort Sea, Alaska
Paul L. Flint, John A. Reed, Deborah Lacroix, Richard Lanctot
2016, Arctic (69) 19-28
From mid-July through September, 10 000 to 30 000 Long-tailed Ducks (Clangula hyemalis) use the lagoon systems of the central Beaufort Sea for remigial molt. Little is known about their foraging behavior and patterns of habitat use during this flightless period. We used radio transmitters to track male Long-tailed Ducks...
Amphibian mortality events and ranavirus outbreaks in the Greater Yellowstone Ecosystem
Debra A. Patla, Sophia St-Hilaire, Andrew P. Rayburn, Blake R. Hossack, Charles R. Peterson
2016, Herpetological Review (47) 50-54
Mortality events in wild amphibians go largely undocumented, and where events are detected, the numbers of dead amphibians observed are probably a small fraction of actual mortality (Green and Sherman 2001; Skerratt et al. 2007). Incidental observations from field surveys can, despite limitations, provide valuable information on the presence, host...
Reevaluating the age of the Walden Creek Group and the kinematic evolution of the western Blue Ridge, southern Appalachians
J. Ryan Thigpen, Robert D. Hatcher Jr., Linda C. Kah, John E. Repetski
2016, American Journal of Science (316) 279-308
An integrated synthesis of existing datasets (detailed geologic mapping, geochronologic, paleontologic, geophysical) with new paleontologic and geochemical investigations of rocks previously interpreted as part of the Neoproterozoic Walden Creek Group in southeastern Tennessee suggest a necessary reevaluation of the kinematics and structural architecture of the Blue Ridge Foothills....
Flow regime effects on mature Populus fremontii (Fremont cottonwood) productivity on two contrasting dryland river floodplains
Douglas C. Andersen
2016, Southwestern Naturalist (61) 8-17
I compared riparian cottonwood (Populus fremontii) productivity-discharge relationships in a relictual stand along the highly regulated Green River and in a naturally functioning stand along the unregulated Yampa River in semiarid northwest Colorado. I used multiple regression to model flow effects on annual basal area increment (BAI) from 1982 to...
Riparian groundwater and baseflow studies in the Upper Colorado River Basin
Lindsay Reynolds, Patrick B. Shafroth
2016, Report, Ruth Powell Hutchins Water Center Scientific and technical report series
Executive summary As part of an ongoing effort to understand baseflow in the Upper Colorado River Basin (UCRB) and implications for stream-dependent ecosystems, we conducted a brief review of literature related to groundwater and baseflow in the UCRB. We included primary literature, federal and state resources, databases and gray literature studies...
Predictive mapping of seabirds, pinnipeds and cetaceans off the Pacific Coast of Washington
Charles Menza, Jeffery B. Leirness, Tim White, Arliss Winship, Brian P. Kinlan, Laura Kracker, Jeannette E. Zamon, Lisa Ballance, Elizabeth Becker, Karin A. Forney, Jay Barlow, Josh Adams, David Pereksta, Scott Pearson, John Pierce, Steven J. Jeffries, John Calambokidis, Annie Douglas, Bradford C. Hanson, Scott R. Benson, Liam Antrim
2016, Report
About this report This report supports Washington-led marine spatial planning and responsible stewardship of natural and cultural resources by the Olympic Coast National Marine Sanctuary. Washington state agencies and the sanctuary continually seek the best available science to improve management of marine uses and stewardship of resources (Etheridge et al., 2010;...
Isotope hydrology of the Chalk River Laboratories site, Ontario, Canada
Zell E. Peterman, Leonid A. Neymark, K.J. King-Sharp, Mel Gascoyne
2016, Applied Geochemistry (66) 149-161
This paper presents results of hydrochemical and isotopic analyses of groundwater (fracture water) and porewater, and physical property and water content measurements of bedrock core at the Chalk River Laboratories (CRL) site in Ontario. Density and water contents were determined and water-loss porosity values were calculated for core samples. Average...
Risk and efficacy of human-enabled interspecific hybridization for climate-change adaptation: Response to Hamilton and Miller (2016)
Ryan P. Kovach, Gordon Luikart, Winsor H. Lowe, Matthew C. Boyer, Clint C. Muhlfeld
2016, Conservation Biology (30) 428-430
Hamilton and Miller (2016) provide an interesting and provocative discussion of how hybridization and introgression can promote evolutionary potential in the face of climate change. They argue that hybridization—mating between individuals from genetically distinct populations—can alleviate inbreeding depression and promote adaptive introgression...
Thorium as a nuclear fuel
Bradley S. Van Gosen, Harikrishnan Tulsidas
Ian Hore-Lacy, editor(s)
2016, Book chapter, Uranium for nuclear power: Resources, mining and transformation to fuel
No abstract available....
Updating movement estimates for American black ducks (Anas rubripes)
Orin J. Robinson, Conor P. McGowan, Patrick K. Devers
2016, PeerJ (4) 1-11
Understanding migratory connectivity for species of concern is of great importance if we are to implement management aimed at conserving them. New methods are improving our understanding of migration; however, banding (ringing) data is by far the most widely available and accessible movement data for researchers. Here, we use band...
Detection of an enigmatic plethodontid Salamander using Environmental DNA
Todd W. Pierson, Anna M. McKee, Stephen F. Spear, John C. Maerz, Carlos D. Camp, Travis C. Glenn
2016, Copeia (104) 78-82
The isolation and identification of environmental DNA (eDNA) offers a non-invasive and efficient method for the detection of rare and secretive aquatic wildlife, and it is being widely integrated into inventory and monitoring efforts. The Patch-Nosed Salamander (Urspelerpes brucei) is a tiny, recently discovered species of plethodontid salamander known only...
Breeding sites and winter site fidelity of Piping Plovers wintering in The Bahamas, a previously unknown major wintering area
Cheri Gratto-Trevor, Susan M. Haig, Mark P. Miller, Thomas D. Mullins, Sidney Maddock, Erin A. Roche, Predensa Moore
2016, Journal of Field Ornithology (87) 29-41
Most of the known wintering areas of Piping Plovers (Charadrius melodus) are along the Atlantic and Gulf coasts of the United States and into Mexico, and in the Caribbean. However, 1066 threatened/endangered Piping Plovers were recently found wintering in The Bahamas, an area not previously known to be important for...
Reduced population variance in strontium isotope values informs domesticated turkey use at Chaco Canyon, New Mexico, USA
Deanna N Grimstead, Amanda C Reynolds, Adam M Hudson, Nancy J Akins, Julio L. Betancourt
2016, Journal of Archaeological Method and Theory (23) 127-149
Traditionally strontium isotopes (87Sr/86Sr) have been used as a sourcing tool in numerous archaeological artifact classes. The research presented here demonstrates that 87Sr/86Srbioapatite ratios also can be used at a population level to investigate the presence of domesticated animals and methods of management. The proposed methodology combines ecology, isotope geochemistry,...
Spatial patterns of native freshwater mussels in the Upper Mississippi River
Patricia R. Ries, Nathan R. De Jager, Steven J. Zigler, Teresa Newton
2016, Freshwater Science (35) 934-947
Multiple physical and biological factors structure freshwater mussel communities in large rivers, and their distributions have been described as clumped or patchy. However, few surveys of mussel populations have been conducted over areas large enough and at resolutions fine enough to quantify spatial patterns in their distribution. We used global...
Vertical deformation associated with normal fault systems evolved over coseismic, postseismic, and multiseismic periods
George A. Thompson, Thomas E. Parsons
2016, Journal of Geophysical Research (121) 2153-2173
Vertical deformation of extensional provinces varies significantly and in seemingly contradictory ways. Sparse but robust geodetic, seismic, and geologic observations in the Basin and Range province of the western United States indicate that immediately after an earthquake, vertical change primarily occurs as subsidence of the normal fault hanging wall. A...
Production of resident fish benefits from experimental salmon subsidies via direct and indirect pathways across stream-riparian boundaries
Scott F. Collins, Colden V. Baxter, Amy M. Marcarelli, Mark S. Wipfli
2016, Ecosphere (7)
Artificial additions of nutrients of differing forms such as salmon carcasses and analog pellets (i.e. pasteurized fishmeal) have been proposed as a means of stimulating aquatic productivity and enhancing populations of anadromous and resident fishes. Nutrient mitigation to enhance fish production in stream ecosystems assumes that the central pathway by...
Progress and challenges in coupled hydrodynamic-ecological estuarine modeling
Neil K. Ganju, Mark J. Brush, Brenda Rashleigh, Alfredo L. Aretxabaleta, Pilar del Barrio, Jason S. Grear, Lora A. Harris, Samuel J. Lake, Grant McCardell, James O'Donnell, David K. Ralston, Richard P. Signell, Jeremy Testa, Jamie M. P. Vaudrey
2016, Estuaries and Coasts (39) 311-332
Numerical modeling has emerged over the last several decades as a widely accepted tool for investigations in environmental sciences. In estuarine research, hydrodynamic and ecological models have moved along parallel tracks with regard to complexity, refinement, computational power, and incorporation of uncertainty. Coupled hydrodynamic-ecological models have been used to assess...
Groundwater conditions in Utah, spring of 2016
Carole B. Burden
2016, Cooperative Investigations Report 57
This is the fifty-third in a series of annual reports that describe groundwater conditions in Utah. Reports in this series, published cooperatively by the U.S. Geological Survey and the Utah Department of Natural Resources, Division of Water Rights, and the Utah Department of Environmental Quality, Division of Water Quality, provide...
Walter Rowe Courtenay, Jr. (1933–2014)
Amy J. Benson
2016, Copeia (104) 297-299
WALTER R. COURTENAY, JR., ichthyologist and retired professor, Florida Atlantic University, Boca Raton, Florida, died in Gainesville, Florida, on 30 January 2014 at age 80. Walt was born in Neenah, Wisconsin, on 6 November 1933, son of Walter and Emily Courtenay. Walt's interest in fish began at a young age...
