sbtools: A package connecting R to cloud-based data for collaborative online research
Luke Winslow, Scott Chamberlain, Alison P. Appling, Jordan S. Read
2016, The R Journal (8) 387-398
The adoption of high-quality tools for collaboration and reproducible research such as R and Github is becoming more common in many research fields. While Github and other version management systems are excellent resources, they were originally designed to handle code and scale poorly to large text-based or binary datasets. A...
Electrofishing effort requirements for estimating species richness in the Kootenai River, Idaho
Carson J. Watkins, Michael C. Quist, Bradley B. Shepard, Susan C. Ireland
2016, Northwest Science (90) 315-327
This study was conducted on the Kootenai River, Idaho to provide insight on sampling requirements to optimize future monitoring effort associated with the response of fish assemblages to habitat rehabilitation. Our objective was to define the electrofishing effort (m) needed to have a 95% probability of sampling 50, 75, and...
The influence of vegetation cover on debris-flow density during an extreme rainfall in the northern Colorado Front Range
Francis K. Rengers, Luke McGuire, Jeffrey A. Coe, Jason W. Kean, Rex L. Baum, Dennis M. Staley, Jonathan W. Godt
2016, Geology (44) 823-826
We explored regional influences on debris-flow initiation throughout the Colorado Front Range (Colorado, USA) by exploiting a unique data set of more than 1100 debris flows that initiated during a 5 day rainstorm in 2013. Using geospatial data, we examined the influence of rain, hillslope angle, hillslope aspect, and vegetation...
Teleconnected ocean forcing of Western North American droughts and pluvials during the last millennium
Cody C. Routson, Connie A. Woodhouse, Jonathan T. Overpeck, Julio L. Betancourt, Nicholas P. McKay
2016, Quaternary Science Reviews (146) 238-250
Western North America (WNA) is rich in hydroclimate reconstructions, yet questions remain about the causes of decadal-to-multidecadal hydroclimate variability. Teleconnection patterns preserved in annually-resolved tree-ring reconstructed drought maps, and anomalies in a global network of proxy sea surface temperature (SST) reconstructions, were used to reassess the evidence linking ocean forcing...
Smokey comes of age: Unmanned aerial systems for fire management
Dirac Twidwell, Craig R. Allen, Carrick Detweiler, James Higgins, Christian Laney, Sebastian Elbaum
2016, Frontiers in Ecology and the Environment (14) 333-339
During the past century, fire management has focused on techniques both to protect human communities from catastrophic wildfire and to maintain fire-dependent ecological systems. However, despite a large and increasing allocation of resources and personnel to achieve these goals, fire management objectives at regional to global scales are not being...
The road to NHDPlus — Advancements in digital stream networks and associated catchments
Richard B. Moore, Thomas A. Dewald
2016, Journal of the American Water Resources Association (52) 890-900
A progression of advancements in Geographic Information Systems techniques for hydrologic network and associated catchment delineation has led to the production of the National Hydrography Dataset Plus (NHDPlus). NHDPlus is a digital stream network for hydrologic modeling with catchments and a suite of related geospatial data. Digital stream networks with...
Overwintering strategies of migratory birds: a novel approach for estimating seasonal movement patterns of residents and transients
Viviana Ruiz-Gutierrez, William L. Kendall, James F. Saracco, Gary C. White
2016, Journal of Applied Ecology (53) 1035-1045
Our understanding of movement patterns in wildlife populations has played an important role in current ecological knowledge and can inform landscape conservation decisions. Direct measures of movement can be obtained using marked individuals, but this requires tracking individuals across a landscape or multiple sites.We demonstrate how movements...
Multispecies cccupancy modeling as a tool for evaluating the status and distribution of Darters in the Elk River, Tennessee
Kathryn M. Potoka, Colin P. Shea, Phillip William Bettoli
2016, Transactions of the American Fisheries Society (145) 1110-1121
Sixteen darter species, including the federally endangered Boulder Darter Etheostoma wapiti, are known to occur in the Elk River, a large, flow-regulated tributary of the Tennessee River, Tennessee–Alabama. Since the construction of Tims Ford Dam (TFD) in 1970, habitat modification caused by cold, hypolimnetic water releases and peak-demand hydropower generation...
Desert bighorn sheep lambing habitat: Parturition, nursery, and predation sites
Rebekah C. Karsch, James W. Cain III, Eric M. Rominger, Elise J. Goldstein
2016, Journal of Wildlife Management (80) 1069-1080
Fitness of female ungulates is determined by neonate survival and lifetime reproductive success. Therefore, adult female ungulates should adopt behaviors and habitat selection patterns that enhance survival of neonates during parturition and lactation. Parturition site location may play an important role in neonatal mortality of desert bighorn sheep (Ovis canadensis...
Considering transient population dynamics in the conservation of slow life-history species: An application to the sandhill crane
Brian D. Gerber, William L. Kendall
2016, Biological Conservation (200) 228-239
The importance of transient dynamics of structured populations is increasingly recognized in ecology, yet these implications are not largely considered in conservation practices. We investigate transient and long-term population dynamics to demonstrate the process and utility of incorporating transient dynamics into conservation research and to better understand the population management...
Measuring, interpreting, and responding to changes in coral reefs: A challenge for biologists, geologist, and managers
Caroline S. Rogers, Jeff Miller
Dennis K. Hubbard, Caroline S. Rogers, Jere H. Lipps, George D. Stanley Jr., editor(s)
2016, Book chapter, Coral reefs at the crossroads
What, exactly, is a coral reef? And how have the world’s reefs changed in the last several decades? What are the stressors undermining reef structure and function? Given the predicted effects of climate change, do reefs have a future? Is it possible to “manage” coral reefs for resilience?...
Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants
Diana A. Stavreva, Lyuba Varticovski, Ludmila Levkova, Anuja A. George, Luke Davis, Gianluca Pegoraro, Vicki S. Blazer, Luke R. Iwanowicz, Gordon L. Hager
2016, Toxicology (368-369) 69-79
Even though the presence of endocrine disrupting chemicals (EDCs) with thyroid hormone (TH)-like activities in the environment is a major health concern, the methods for their efficient detection and monitoring are still limited. Here we describe a novel cell assay, based on the translocation of a green fluorescent protein (GFP)—tagged...
The Mississippi River: A place for fish
Harold Schramm, Brian Ickes
Yushun Chen, Duane Chapman, John Jackson, Daqing Chen, Zhongjie Li, Jack Kilgore, Quinton E. Phelps, Michael Eggleton, editor(s)
2016, Book chapter, Fishery Resources, Environment, and Conservation in the Mississippi and Yangtze (Changjiang) River Basins
The Mississippi River flows 3,734 km from its source at Lake Itasca, Minnesota to its outlet at the Gulf of Mexico. Along its course, it collects water from portions of two Canadian provinces and 41 % of the conterminous United States. Although greatly altered for navigation and flood control throughout...
Effects of spray-dried Pseudomonas fluorescens, strain CL145A (Zequanox®) on reproduction and early development of the fathead minnow (Pimephales promelas).
Diane L. Waller, James A. Luoma
2016, Report
The biopesticide, Zequanox®, is registered for dreissenid mussel control in open water systems. Previous toxicity trials with nontarget organisms, including young-of-the year of several fish species and invertebrates, demonstrated selectivity of Zequanox for dreissenids. However, data are lacking on its safety to reproductive and early life stages of fish. The...
Noncontact methods for measuring water-surface elevations and velocities in rivers: Implications for depth and discharge extraction
Jonathan M. Nelson, Paul J. Kinzel, Richard R. McDonald, Mark Schmeeckle
2016, Conference Paper, RiverFlow 2016
Recently developed optical and videographic methods for measuring water-surface properties in a noninvasive manner hold great promise for extracting river hydraulic and bathymetric information. This paper describes such a technique, concentrating on the method of infrared videog- raphy for measuring surface velocities and both acoustic (laboratory-based) and laser-scanning (field-based) techniques for...
Comment on “Geochemistry of buried river sediments from Ghaggar Plains, NW India: Multi-proxy records of variations in provenance, paleoclimate, and paleovegetation patterns in the late quaternary” by Ajit Singh, Debajyoti Paul, Rajiv Sinha, Kristina J. Thomsen, Sanjeev Gupta
Peter D. Clift, Liviu Giosan, Amy E. East
2016, Palaeogeography, Palaeoclimatology, Palaeoecology (455) 65-67
Singh et al. (2016) published a geochemical record of sediment compositions from the flood plain of the Ghaggar River in western India and use the changing provenance, particularly as traced by Nd isotope composition, to reconstruct how erosion patterns have changed over the past 100 k.y. In doing so they...
Advancing environmental flow science: Developing frameworks for altered landscapes and integrating efforts across disciplines.
Shannon K. Brewer, Ryan A. McManamay, Andrew D. Miller, Robert Mollenhauer, Thomas A. Worthington, Tom Arsuffi
2016, Environmental Management (58) 175-192
Environmental flows represent a legal mechanism to balance existing and future water uses and sustain non-use values. Here, we identify current challenges, provide examples where they are important, and suggest research advances that would benefit environmental flow science. Specifically, environmental flow science would benefit by (1) developing approaches...
Seasonal movements and habitat use of Potamodromous Rainbow Trout across a complex Alaska riverscape
Kevin M. Fraley, Jeffrey A. Falke, Richard Yanusz, Sam S. Ivey
2016, Transactions of the American Fisheries Society (145) 1077-1092
Potamodromous Rainbow Trout Oncorhynchus mykiss are an important ecological and recreational resource in freshwater ecosystems of Alaska, and increased human development, hydroelectric projects, and reduced escapement of Chinook Salmon Oncorhynchus tshawytscha may threaten their populations. We used aerial and on-the-ground telemetry tracking, a digital landscape model, and resource selection functions...
Responses of a tall building in Los Angeles, California as inferred from local and distant earthquakes
Mehmet Çelebi, Hasan Ulusoy, Nori Nakata
2016, Earthquake Spectra (32) 1821-1843
Increasing inventory of tall buildings in the United States and elsewhere may be subjected to motions generated by near and far seismic sources that cause long-period effects. Multiple sets of records that exhibited such effects were retrieved from tall buildings in Tokyo and Osaka ~ 350 km and 770 km...
Damage and recovery assessment of the Philippines' mangroves following Super Typhoon Haiyan
Jordan Long, Chandra Giri, Jurgene H. Primavera, Mandar Trivedi
2016, Marine Pollution Bulletin (109) 734-743
We quantified mangrove disturbance resulting from Super Typhoon Haiyan using a remote sensing approach. Mangrove areas were mapped prior to Haiyan using 30 m Landsat imagery and a supervised decision-tree classification. A time sequence of 250 m eMODIS data was used to monitor mangrove condition prior to, and following, Haiyan. Based on...
Carbon and energy fluxes in cropland ecosystems: a model-data comparison
E. Lokupitiya, A. Scott Denning, K. Schaefer, D. Ricciuto, R. Anderson, M. A. Arain, I. Baker, A. G. Barr, G. Chen, J.M. Chen, P. Ciais, D.R. Cook, M.C. Dietze, M. El Maayar, M. Fischer, R. Grant, D. Hollinger, C. Izaurralde, A. Jain, C.J. Kucharik, Z. Li, S. Liu, L. Li, R. Matamala, P. Peylin, D. Price, S. W. Running, A. Sahoo, M. Sprintsin, A.E. Suyker, H. Tian, Christina Tonitto, M.S. Torn, Hans Verbeeck, S.B. Verma, Y. Xue
2016, Biogeochemistry (128) 53-76
Croplands are highly productive ecosystems that contribute to land–atmosphere exchange of carbon, energy, and water during their short growing seasons. We evaluated and compared net ecosystem exchange (NEE), latent heat flux (LE), and sensible heat flux (H) simulated by a suite of ecosystem models at five agricultural eddy covariance flux...
Spawning and hatching of endangered Gila Chub in captivity
Andrew A. Schultz, Scott A. Bonar
2016, North American Journal of Aquaculture (78) 279-283
Information on reproductive characteristics of the endangered Gila Chub Gila intermedia is largely limited and qualitative, and culture techniques and requirements are virtually unknown. Here we provide the first published data on spawning and selected reproductive and developmental characteristics of Gila Chub. Fish were brought to the laboratory in March...
Origin of the pulse-like signature of shallow long-period volcano seismicity
Bernard A. Chouet, Phillip B. Dawson
2016, Journal of Geophysical Research B: Solid Earth (121) 5931-5941
Short-duration, pulse-like long-period (LP) events are a characteristic type of seismicity accompanying eruptive activity at Mount Etna in Italy in 2004 and 2008 and at Turrialba Volcano in Costa Rica and Ubinas Volcano in Peru in 2009. We use the discrete wave number method to compute the free surface response...
Coseismic slip and early afterslip of the 2015 Illapel, Chile, earthquake: Implications for frictional heterogeneity and coastal uplift
William D. Barnhart, Jessica R. Murray, Richard W. Briggs, Francisco Gomez, Charles P. J. Miles, Jerry L. Svarc, Sebástian Riquelme, Bryan J. Stressler
2016, Journal of Geophysical Research B: Solid Earth (121) 6172-6191
Great subduction earthquakes are thought to rupture portions of the megathrust, where interseismic coupling is high and velocity-weakening frictional behavior is dominant, releasing elastic deformation accrued over a seismic cycle. Conversely, postseismic afterslip is assumed to occur primarily in regions of velocity-strengthening frictional characteristics that may correlate with lower interseismic...
Observations and modeling of fjord sedimentation during the 30 year retreat of Columbia Glacier, AK
Katherine B Love, Bernard Hallet, Thomas L. Pratt, Shad O’Neel
2016, Journal of Glaciology (62) 778-793
To explore links between glacier dynamics, sediment yields and the accumulation of glacial sediments in a temperate setting, we use extensive glaciological observations for Columbia Glacier, Alaska, and new oceanographic data from the fjord exposed during its retreat. High-resolution seismic data indicate that 3.2 × 108 m3 of...
