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Publication Extents

Not all publications have extents, not all extents are completely accurate
Implications of water, sediment, and nutrient budgets for the restoration of a shallow, turbid lake in semiarid southeastern Oregon
Cassandra D. Smith, Tamara M. Wood
2023, Scientific Investigations Report 2023-5098
Malheur Lake is the largest lake in the endorheic Harney Basin in southeastern Oregon. Since the 1990s, Malheur Lake—which averages depths of about 1 meter—has been in a degraded, turbid state lacking submergent and emergent vegetation. The goals of this study were to identify the major sources of sediment and...
Application of a catch multiple survey analysis for Atlantic horseshoe crab Limulus polyphemus in the Delaware Bay
Kristen A. Anstead, John A. Sweka, Linda Barry, Eric M. Hallerman, David R. Smith, Natalie Ameral, Michael Schmidtke, Richard A. Wong
2023, Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science (15)
ObjectiveThis paper applies a catch multiple survey analysis (CMSA) to Atlantic horseshoe crabs Limulus polyphemus in the Delaware Bay to generate robust population estimates for harvest management. Currently, horseshoe crabs along the U.S. Atlantic coast are harvested as bait for other fisheries and collected for their blood, which is...
Assessment of recovery potential for the American horseshoe crab (Limulus polyphemus): An application of the IUCN green status process
David R. Smith, H. Jane Brockmann, Ruth H. Carmichael, Eric M. Hallerman, W.M. Watson, Jaime Zaldivar-Rae
2023, Aquatic Conservation: Marine and Freshwater Ecosystems
According to an International Union for Conservation of Nature (IUCN) Red List assessment (RLA), the American horseshoe crab (Limulus polyphemus), an iconic coastal species, is at risk of extirpation in some regions within its range where small and vulnerable populations occur. However, the RLA does not consider future status...
Movement and behavioral states of common carp (Cyprinus carpio) in response to a behavioral deterrent in a navigational lock
Maggie Jo Raboin, John Plumb, Matthew Sholtis, David Smith, P. Ryan Jackson, Jose Rivera, Cory D. Suski, Aaron R. Cupp
2023, Movement Ecology (11)
Freshwater ecosystems are some of the most affected by biological invasions due, in part, to the introduction of invasive carp worldwide. Where carp have become established, management programs often seek to limit further range expansion into new areas by reducing their movement through interconnected rivers and waterways. Lock and dams...
Postfire hydrologic response along the central California (USA) coast: Insights for the emergency assessment of postfire debris-flow hazards
Matthew A. Thomas, Jason W. Kean, Scott W. McCoy, Donald N. Lindsay, Jaime Kostelnik, David B. Cavagnaro, Francis K. Rengers, Amy E. East, Jonathan Schwartz, Douglas P. Smith, Brian D. Collins
2023, Landslides
The steep, tectonically active terrain along the Central California (USA) coast is well known to produce deadly and destructive debris flows. However, the extent to which fire affects debris-flow susceptibility in this region is an open question. We documented the occurrence of postfire debris floods and flows following the landfall...
A detailed view of the 2020-2023 southwestern Puerto Rico seismic sequence with deep learning
Clara Yoon, Elizabeth S. Cochran, Elizabeth A. Vanacore, Victor Huerfano, Gisela Báez-Sánchez, John D. Wilding, Jonathan D. Smith
2023, Bulletin of the Seismological Society of America
The 2020–2023 southwestern Puerto Rico seismic sequence, still ongoing in 2023, is remarkable for its multiple‐fault rupture complexity and elevated aftershock productivity. We applied an automatic workflow to continuous data from 43 seismic stations in Puerto Rico to build an enhanced earthquake catalog with ∼180,000 events for the 3+ yr...
The unmarked R package: Twelve years of advances in occurrence and abundance modelling in ecology
Kenneth F. Kellner, Adam D. Smith, J. Andrew Royle, Marc Kéry, Jerrold L. Belant, Richard B. Chandler
2023, Methods in Ecology & Evolution (14) 1408-1415
Species distribution models (SDMs) are widely applied to understand the processes governing spatial and temporal variation in species abundance and distribution but often do not account for measurement errors such as false negatives and false positives.We describe unmarked, a package for the freely available and open-source R software that provides...
A science and management partnership to restore coregonine diversity to the Laurentian Great Lakes
David Bunnell, Amanda Susanne Ackiss, Karen M Alofs, Cory Brant, Charles R. Bronte, Randall M. Claramunt, John M. Dettmers, Andrew Edgar Honsey, Nicholas E. Mandrak, Andrew M. Muir, Victor Santucci, David R. Smith, Russell M. Strach, John A. Sweka, Brian C. Weidel, William Mattes, Kurt R. Newman
2023, Environmental Reviews
Similar to many freshwater ecosystems, the Laurentian Great Lakes of North America have undergone numerous anthropogenic stressors resulting in considerable loss of biodiversity and habitat. Among Great Lakes fishes, the coregonine sub-family has endured the most extensive declines, including extinction of several species (Coregonus johannae, C. alpenae,...
When are environmental DNA early detections of invasive species actionable?
Adam J. Sepulveda, Christine E. Dumoulin, Denise L. Blanchette, John Mcphedran, Colin Holme, Nathan Whalen, Margaret Hunter, Christopher M. Merkes, Catherine A. Richter, Matthew Neilson, Wesley Daniel, Devin Nicole Jones, David R. Smith
2023, Journal of Environmental Management (343)
Environmental DNA (eDNA) sampling provides sensitive early detection capabilities for recently introduced taxa. However, natural resource managers struggle with how to integrate eDNA results into an early detection rapid response program because positive eDNA detections are not always indicative of...
Creating conservation strategies with value-focused thinking
David M. Martin, Joshua Goldstein, David R. Smith, Jessica Musengezi, Jessie G. Rountree, Pabodha G. A. Galgamuwe, Aileen Craig, Michelle Dietz, Caitlin Kerr
2023, Conservation Biology
Biodiversity and human well-being strategies are only as good as the set of ideas that people think about. This article evaluates value-focused thinking (VFT), a framework that focuses on creating objectives and strategy ideas that are responsive to the objectives. We performed a proof-of-concept study of VFT on six planning...
Six years of fluvial response to a large dam removal on the Carmel River, California, USA
Amy E. East, Lee R. Harrison, Douglas P. Smith, Joshua B. Logan, Rosealea Bond
2023, Earth Surface Processes and Landforms (48) 1487-1501
Measuring river response to dam removal affords a rare, important opportunity to study fluvial response to sediment pulses on a large field scale. We present a before–after/control–impact study of the Carmel River, California, measuring fluvial geomorphic and grain-size evolution over 8 years, six of which postdated removal of a 32 m-high...
Incorporating temperature into seepage loss estimates for a large unlined irrigation canal
Ramon C. Naranjo, David Smith, Evan J. Lindenbach
2023, Journal of Hydrology (617)
Quantifying seepage losses from unlined irrigation canals is necessary to improve water use and conservation. The use of heat as a tracer is widely used in quantifying seepage rates across the sediment–water interface. In this study, field observations and two-dimensional numerical models...
Expert perspectives on global biodiversity loss and its drivers and impacts on people
Forest Isbell, Patricia Balvanera, Akira S. Mori, Jin-Sheng He, James M. Bullock, Ganga Ram Regmi, Eric W. Seabloom, Simon Ferrier, Osvaldo E. Sala, Nathaly R. Guerrero-Ramírez, Julia Tavella, Daniel J. Larkin, Bernhard Schmid, Charlotte L. Outhwaite, Pairot Pramua, Elizabeth T. Borer, Michel Loreau, Taiwo Crossby Omotoriogun, David O. Obura, Maggie Anderson, Cristina Portales-Reyes, Kevin Kirkman, Pablo M Vergara, Adam Thomas Clark, Kimberly J Komatsu, Owen L. Petchey, Sarah R. Weiskopf, Laura J. Williams, Scott L. Collins, Nico Eisenhauer, Christopher H Trisos, Delphine Renard, Alexandra J. Wright, Poonam Tripathi, Jane Cowles, Jarrett E. K. Byrnes, Peter B. Reich, Andy Purvis, Zati Sharip, Mary I. O'Connor, Clare E. Kazanski, Nick M. Haddad, Eulogio H. Soto, Laura E. Dee, Sandra Díaz, Chad R. Zirbel, Meghan L. Avolio, Shaopeng Wang, Zhiyuan Ma, Jingjing Liang, Hanan C. Farah, Justin Andrew Johnson, Brian W. Miller, Yann Hautier, Melinda D. Smith, Johannes M. H. Knops, Bonnie Myers, Zuzana Harmáčková, Jorge Cortés, Mike Harfoot, Andrew Gonzalez, Tim Newbold, Jacqueline Oehri, Marina Mazón, Cynnamon Dobbs, Meredith S. Palmer
2023, Frontiers in Ecology and the Environment (21) 94-103
Despite substantial progress in understanding global biodiversity loss, major taxonomic and geographic knowledge gaps remain. Decision makers often rely on expert judgement to fill knowledge gaps, but are rarely able to engage with sufficiently large and diverse groups of specialists. To improve understanding of the perspectives of thousands of biodiversity...
North American Bat Monitoring Program (NABat) mobile acoustic transect surveys standard operating procedure 1—Locating and establishing mobile transect routes
Jaclyn Martin, Dane Smith, Han Li, MacKenzie Hall, Emily Ferrall, Jason Rae, Bethany Straw, Brian Reichert
2022, Techniques and Methods 2-C1
This document is the first of three standard operating procedures (SOPs) providing instructions and considerations for conducting mobile acoustic surveys along road transects to collect bat acoustic data following the North American Bat Monitoring Program (NABat) protocol and sample design. This SOP focuses specifically on selecting NABat grid cells and...
Horseshoe crab
David R. Smith
2022, Book chapter, Technical report for the Delaware estuary and basin, PDE Report No. 22-05
No abstract available....
Evaluating noninvasive methods for estimating cestode prevalence in a wild carnivore population
E E Brandell, M.K. Jackson, Paul C. Cross, A.J. Piaggio, D. R. Taylor, Douglas W. Smith, B Boufana, Daniel R. Stahler, PJ Hudson
2022, PLoS ONE (17)
Helminth infections are cryptic and can be difficult to study in wildlife species. Helminth research in wildlife hosts has historically required invasive animal handling and necropsy, while results from noninvasive parasite research, like scat analysis, may not be possible at the helminth species or individual host...
Disease outbreaks select for mate choice and coat color in wolves
Sarah Cubaynes, E E Brandell, Daniel R. Stahler, Douglas W. Smith, Emily S. Almberg, Susanne Schindler, Robert K. Wayne, Andrew P. Dobson, Bridgett M. vonHoldt, Daniel R. MacNulty, Paul C. Cross, Peter J. Hudson, Tim Coulson
2022, Science (378) 300-303
We know much about pathogen evolution and the emergence of new disease strains, but less about host resistance and how it is signaled to other individuals and subsequently maintained. The cline in frequency of black-coated wolves (Canis lupus) across North America is hypothesized to result from a relationship with canine...
Multispecies approaches to status assessments in support of endangered species classifications
Daniel Bruce Fitzgerald, Mary Freeman, Kelly O. Maloney, John A. Young, Amanda E. Rosenberger, David C. Kazyak, David R. Smith
2022, Conservation Science and Practice (4)
Multispecies risk assessments have developed within many international conservation programs, reflecting a widespread need for efficiency. Under the United States Endangered Species Act (ESA), multispecies assessments ultimately lead to species-level listing decisions. Although this approach provides opportunities for improved efficiency, it also risks overwhelming or biasing the assessment process and...
Potential effects of energy development on environmental resources of the Williston Basin in Montana, North Dakota, and South Dakota—Water resources
Timothy T. Bartos, Steven K. Sando, Todd M. Preston, Gregory C. Delzer, Robert F. Lundgren, Rochelle A. Nustad, Rodney R. Caldwell, Zell E. Peterman, Bruce D. Smith, Kathleen M. Macek-Rowland, David A. Bender, Jill D. Frankforter, Joel M. Galloway
2022, Scientific Investigations Report 2017-5070-C
The Williston Basin has been a leading oil and gas producing area for more than 50 years. While oil production initially peaked within the Williston Basin in the mid-1980s, production rapidly increased in the mid-2000s, largely because of improved horizontal (directional) drilling and hydraulic fracturing methods. In 2012, energy development...
Light attenuation and erosion characteristics of fine sediments in a highly turbid, shallow, Great Basin Lake—Malheur Lake, Oregon, 2017–18
Tamara M. Wood, Cassandra D. Smith
2022, Scientific Investigations Report 2022-5056
Malheur Lake is a large, shallow, turbid lake in southeastern Oregon that fluctuates widely in surface area in response to yearly precipitation and climatic cycles. High suspended-sediment concentrations (SSCs) likely are negatively affecting the survival of aquatic plants by reducing the intensity of solar radiation reaching the plants, thus...
Potential effects of sea level rise on nearshore habitat availability for surf smelt (Hypomesus pretiosus) and eelgrass (Zostera marina), Puget Sound, Washington
Collin D. Smith, Theresa L. Liedtke
2022, Open-File Report 2022-1054
In this study we examine the potential effects of three predicted sea level rise (SLR) scenarios on the nearshore eelgrass (Zostera marina L.) and surf smelt (Hypomesus pretiosus) spawning habitats along a beach on Bainbridge Island, Washington. Baseline bathymetric, geomorphological, and biological surveys were conducted to determine the existing...
Using structured decision making to evaluate potential management responses to detection of dreissenid mussel (Dreissena spp.) environmental DNA
Adam J. Sepulveda, David R. Smith, Katherine M O'Donnell, Nathan Owens, Brittany White, Catherine A. Richter, Christopher M. Merkes, Skylar Wolf, Mike Rau, Matthew Neilson, Wesley Daniel, Christine E. Dumoulin, Margaret Hunter
2022, Management of Biological Invasions (13) 344-368
Environmental (e)DNA tools are sensitive and cost-effective for early detection of invasive species. However, the uncertainty associated with the interpretation of positive eDNA detections makes it challenging to determine appropriate natural resource management responses. Multiple sources of error can give rise to positive detections of eDNA in a sample when...
Monitoring fish abundance and behavior, using multi-beam acoustic imaging sonar, at a Selective Water Withdrawal structure in Lake Billy Chinook, Deschutes River, Oregon, 2020
Collin D. Smith, Tyson W. Hatton, Noah S. Adams
2022, Open-File Report 2022-1038
Collection of juvenile salmonids at Round Butte Dam is a critical part of the effort to enhance populations of anadromous fish species in the upper Deschutes River because fish that are not collected at the dam may either incur increased mortality during dam passage or remain landlocked and lost...
Status and trends of North American bats: Summer occupancy analysis 2010-2019
Bradley James Udell, Bethany Straw, Tina L. Cheng, Kyle Enns, Winifred F. Frick, Benjamin Gotthold, Kathryn Irvine, Cori Lausen, Susan Loeb, Jonathan D. Reichard, Thomas J. Rodhouse, Dane Smith, Christian Stratton, Wayne E. Thogmartin, Brian Reichert
2022, Report
• We developed an analytical pipeline supported by web-based infrastructure for integrating continental scale bat monitoring data (stationary acoustic, mobile acoustic, and capture records) to estimate summer (May 1–Aug 31) occupancy probabilities and changes in occupancy over time for 12 North American bat species. This serves as one of multiple...