A guide to Bayesian model checking for ecologists
Paul B. Conn, Devin S. Johnson, Perry J. Williams, Sharon R. Melin, Mevin Hooten
2018, Ecological Monographs (88) 526-542
Checking that models adequately represent data is an essential component of applied statistical inference. Ecologists increasingly use hierarchical Bayesian statistical models in their research. The appeal of this modeling paradigm is undeniable, as researchers can build and fit models that embody complex ecological processes while simultaneously accounting for observation error....
Science support for evaluating natural recovery of polychlorinated biphenyl concentrations in fish from Crab Orchard Lake, Crab Orchard National Wildlife Refuge, Illinois
Bethany K. Kunz, Jo Ellen Hinck, Robin D. Calfee, Greg L. Linder, Edward E. Little
2018, Open-File Report 2018-1006
IntroductionCrab Orchard Lake in southern Illinois is one of the largest and most popular recreational lakes in the state. Construction of the nearly 7,000-acre reservoir in the late 1930s created employment opportunities through the Works Progress Administration, and the lake itself was intended to supply water, control flooding, and provide...
Preliminary synthesis and assessment of environmental flows in the middle Verde River watershed, Arizona
Nicholas V. Paretti, Anne M. D. Brasher, Susanna L. Pearlstein, Dena M. Skow, Bruce Gungle, Bradley D. Garner
2018, Scientific Investigations Report 2017-5100
A 3-year study was undertaken to evaluate the suitability of the available modeling tools for characterizing environmental flows in the middle Verde River watershed of central Arizona, describe riparian vegetation throughout the watershed, and estimate sediment mobilization in the river. Existing data on fish and macroinvertebrates were analyzed in relation...
Landscape‐level patterns in fawn survival across North America
Tess M. Gingery, Duane R. Diefenbach, Bret D. Wallingford, Christopher S. Rosenberry
2018, Journal of Wildlife Management (82) 1003-1013
A landscape‐level meta‐analysis approach to examining early survival of ungulates may elucidate patterns in survival not evident from individual studies. Despite numerous efforts, the relationship between fawn survival and habitat characteristics remains unclear and there has been no attempt to examine trends in survival across landscape types with adequate replication....
Hydrologic characteristics of freshwater mussel habitat: novel insights from modeled flows
C. Ashton Drew, Michele Eddy, Thomas J. Kwak, W. Gregory Cope, Tom Augspurger
2018, Freshwater Science (37) 343-356
The ability to model freshwater stream habitat and species distributions is limited by the spatially sparse flow data available from long-term gauging stations. Flow data beyond the immediate vicinity of gauging stations would enhance our ability to explore and characterize hydrologic habitat suitability. The southeastern USA supports high aquatic biodiversity,...
Respiratory disease, behavior, and survival of mountain goat kids
Julie A. Blanchong, Christopher A. Anderson, Nicholas J. Clark, Robert W. Klaver, Paul J. Plummer, Mike Cox, Caleb Mcadoo, Peregrine L. Wolff
2018, Journal of Wildlife Management (82) 1243-1251
Bacterial pneumonia is a threat to bighorn sheep (Ovis canadensis) populations. Bighorn sheep in the East Humboldt Mountain Range (EHR), Nevada, USA, experienced a pneumonia epizootic in 2009–2010. Testing of mountain goats (Oreamnos americanus) that were captured or found dead on this range during and after the epizootic detected bacteria...
Development and characterization of 12 polymorphic microsatellite loci in the sea sandwort, Honckenya peploides
Megan C. Gravley, George K. Sage, Sandra L. Talbot, Matthew L. Carlson
2018, Journal of Plant Research (131) 879-885
Codominant marker systems are better suited to analyze population structure and assess the source of an individual in admixture analyses. Currently, there is no codominant marker system using microsatellites developed for the sea sandwort, Honckenya peploides (L.) Ehrh., an early colonizer in island systems. We developed and characterized...
Estimates of long-term mean-annual nutrient loads considered for use in SPARROW models of the Midcontinental region of Canada and the United States, 2002 base year
David A. Saad, Glenn A. Benoy, Dale M. Robertson
2018, Scientific Investigations Report 2018-5051
Streamflow and nutrient concentration data needed to compute nitrogen and phosphorus loads were compiled from Federal, State, Provincial, and local agency databases and also from selected university databases. The nitrogen and phosphorus loads are necessary inputs to Spatially Referenced Regressions on Watershed Attributes (SPARROW) models. SPARROW models are a way...
Examining speed versus selection in connectivity models using elk migration as an example
Angela Brennan, Ephraim M. Hanks, Jerod Merkle, Eric K. Cole, Sarah Dewey, Alyson B. Courtemanch, Paul C. Cross
2018, Landscape Ecology (33) 955-968
ContextLandscape resistance is vital to connectivity modeling and frequently derived from resource selection functions (RSFs). RSFs estimate relative probability of use and tend to focus on understanding habitat preferences during slow, routine animal movements (e.g., foraging). Dispersal and migration, however, can produce rarer, faster movements,...
Groundwater-quality data from the eastern Snake River Plain Aquifer, Jerome and Gooding Counties, south-central Idaho, 2017
Kenneth D. Skinner
2018, Data Series 1085
Groundwater-quality samples and water-level data were collected from 36 wells in the Jerome/Gooding County area of the eastern Snake River Plain aquifer during June 2017. The wells included 30 wells sampled for the U.S. Geological Survey’s National Water-Quality Assessment project, plus an additional 6 wells were selected to increase...
Measuring and evaluating ecological flows from streams to regions: Steps towards national coverage
James E. McKenna Jr., Howard W. Reeves, Paul Seelbach
2018, Freshwater Biology (63) 874-890
Living aquatic communities are largely determined and maintained by the volume and quality of flowing waters, both within lotic systems and in receiving waters of coastal systems. However, flow is one of the most frequently and extensively altered features of rivers and streams; alteration effects are likely to be...
U.S. Geological Survey science for the Wyoming Landscape Conservation Initiative—2016 annual report
Zachary H. Bowen, Ellen Aikens, Cameron L. Aldridge, Patrick J. Anderson, Timothy J. Assal, Anna D. Chalfoun, Geneva W. Chong, Cheryl A. Eddy-Miller, Steven L. Garman, Steve Germaine, Collin G. Homer, Aaron N. Johnston, Matthew J. Kauffman, Daniel J. Manier, Cynthia P. Melcher, Kirk A. Miller, Annika W. Walters, Jerrod D. Wheeler, Daniel J. Wieferich, Anna B. Wilson, Teal B. Wyckoff, Linda Zeigenfuss
2018, Open-File Report 2018-1048
This is the ninth annual report highlighting U.S. Geological Survey (USGS) science and decision-support activities conducted for the Wyoming Landscape Conservation Initiative (WLCI). The activities address specific management needs identified by WLCI partner agencies. In fiscal year (FY) 2016, there were 26 active USGS WLCI science-based projects. Of these 26...
The complete mitochondrial genome of Hine’s emerald dragonfly (Somatochlora hineana Williamson) via NGS sequencing
Craig Jackson, S. Grace McCalla, Jon Amberg, Daniel Soluk, Hugh Britten
2018, Mitochondrial DNA Part B (3) 562-563
Here, we report the complete mitochondrial genome of the endangered Hine’s emerald dragonfly (HED), Somatochlora hineana Williamson. Data were generated via next generation sequencing (NGS) and assembled using a mitochondrial baiting and iterative mapping approach. The full length circular genome is 15,705 bp with 26.6% GC content. It contains the typical metazoan set...
An initial validation of Landsat 5 and 7 derived surface water temperature for U.S. lakes, reservoirs, and estuaries
Blake A. Schaeffer, John Iiames, John L. Dwyer, Erin Urquhart, Wilson Salls, Jennifer Rover, Bridget Seegers
2018, International Journal of Remote Sensing (39) 7789-7805
The United States Harmful Algal Bloom and Hypoxia Research Control Act of 2014 identified the need for forecasting and monitoring harmful algal blooms (HAB) in lakes, reservoirs, and estuaries across the nation. Temperature is a driver in HAB forecasting models that affects both HAB growth rates and toxin production. Therefore,...
Integrated analysis for population estimation, management impact evaluation, and decision-making for a declining species
Brian A. Crawford, Clinton T. Moore, Terry M. Norton, John C. Maerz
2018, Biological Conservation (222) 33-43
A challenge for making conservation decisions is predicting how wildlife populations respond to multiple, concurrent threats and potential management strategies, usually under substantial uncertainty. Integrated modeling approaches can improve estimation of demographic rates necessary for making predictions, even for rare or cryptic species with sparse data, but their use in...
Use of non-invasive genetics to generate core-area population estimates of a threatened predator in the Superior National Forest, USA
Shannon Barber-Meyer, Daniel Ryan, David Grosshuesch, Timothy Catton, Sarah Malick-Wahls
2018, Canadian Wildlife Biology and Management (7) 46-55
Canada lynx (Lynx canadensis) are found in boreal forests of Canada and Alaska and range southward into the contiguous United States. Much less is understood about lynx in their southern range compared to northern populations. Because lynx are currently listed as threatened under the US Endangered Species Act but have...
Methods for peak-flow frequency analysis and reporting for streamgages in or near Montana based on data through water year 2015
Steven K. Sando, Peter M. McCarthy
2018, Scientific Investigations Report 2018-5046
This report documents the methods for peak-flow frequency (hereinafter “frequency”) analysis and reporting for streamgages in and near Montana following implementation of the Bulletin 17C guidelines. The methods are used to provide estimates of peak-flow quantiles for 50-, 42.9-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities...
Incorporating road crossing data into vehicle collision risk models for moose (Alces americanus) in Massachusetts, USA
Katherine Zeller, David Wattles, Stephen Destefano
2018, Environmental Management (62) 518-528
Wildlife–vehicle collisions are a human safety issue and may negatively impact wildlife populations. Most wildlife–vehicle collision studies predict high-risk road segments using only collision data. However, these data lack biologically relevant information such as wildlife population densities and successful road-crossing locations. We overcome this shortcoming with a new method that...
Compilation and analysis of multiple groundwater-quality datasets for Idaho
Stephen A. Hundt, Candice B. Hopkins
2018, Open-File Report 2018-1079
Groundwater is an important source of drinking and irrigation water throughout Idaho, and groundwater quality is monitored by various Federal, State, and local agencies. The historical, multi-agency records of groundwater quality include a valuable dataset that has yet to be compiled or analyzed on a statewide level. The purpose...
Rethinking the use of seabed sediment temperature profiles to trace submarine groundwater flow
Barret L. Kurylyk, Dylan J. Irvine, A.A. Mohammed, V. F. Bense, Martin A. Briggs, J.W. Loder, Y. Geshelin
2018, Water Resources Research (54) 4595-4614
Submarine groundwater fluxes across the seafloor facilitate important hydrological and biogeochemical exchanges between oceans and seabed sediment, yet few studies have investigated spatially distributed groundwater fluxes in deep‐ocean environments such as continental slopes. Heat has been previously applied as a submarine groundwater tracer using an analytical solution to a heat...
A snow density dataset for improving surface boundary conditions in Greenland ice sheet firn modeling
Robert Fausto, Jason E. Box, Baptiste Vandecrux, Dirk van As, Konrad Steffen, Michael J. MacFerrin, Horst Machguth, William Colgan, Daniel Mcgrath, Lora S. Koenig, Charalampos Charalampidis, Roger J. Braithwaite
2018, Frontiers in Earth Science (6)
The surface snow density of glaciers and ice sheets is of fundamental importance in converting volume to mass in both altimetry and surface mass balance studies, yet it is often poorly constrained. Site-specific surface snow densities are typically derived from empirical relations based on temperature and wind speed. These parameterizations...
Separable correlation and maximum likelihood
Karl Oskar Ekvall, Brian R. Gray
2018, arXiv
We consider estimation of the covariance matrix of a multivariate normal distribution when the correlation matrix is separable in the sense that it factors as a Kronecker product of two smaller matrices. A computationally convenient coordinate descent-type algorithm is developed for maximum likelihood estimation. Simulations indicate our method often gives...
Modeling the fish community population dynamics and forecasting the eradication success of an exotic fish from an alpine stream
Christophe Laplanche, Arnaud Elger, Frederic Santoul, Gary P. Thiede, Phaedra E. Budy
2018, Biological Conservation (223) 34-46
Management actions aimed at eradicating exotic fish species from riverine ecosystems can be better informed by forecasting abilities of mechanistic models. We illustrate this point with an example of the Logan River, Utah, originally populated with endemic cutthroat trout (Oncorhynchus clarkii utah), which compete with...
Hydrologic and water-quality characteristics of Caño Boquerón, Cabo Rojo, and Puerto Mosquito, Isla de Vieques, Puerto Rico, July 2015–July 2016
Julieta M. Gómez-Fragoso, Jose A. Santiago-Saez
2018, Scientific Investigations Report 2018-5018
Coastal lagoons are common features of the Puerto Rico shoreline that provide habitat for commercial and recreational species and serve important roles in the nutrient cycle of the ecosystems. The U.S. Geological Survey, in cooperation with the Puerto Rico Environmental Quality Board, conducted a limnological study at Caño Boquerón in...
Crustal structure and quaternary acceleration of deformation rates in central Washington revealed by stream profile inversion, potential field geophysics, and structural geology of the Yakima folds
Lydia M. Staisch, Richard J. Blakely, Harvey Kelsey, Richard Styron, Brian L. Sherrod
2018, Tectonics (37) 1750-1770
Post‐Miocene tectonic uplift along fault‐cored anticlines within central Washington produced the Yakima Fold Province, a region of active NNE‐SSW shortening in the Cascadian backarc. The relative timing and rate of deformation along individual structures is coarsely defined yet imperative for seismic hazard assessment. In this work, we use geomorphic and...
