New diagnostic assessment of MCMC algorithm effectiveness, efficiency, reliability, and controllability
Hossein KavianiHamedani, Julianne D. Quinn, Jared David Smith
2024, IEEE Access (12) 42385-42400
Markov Chain Monte Carlo (MCMC) is a robust statistical approach for estimating posterior distributions. However, the significant computational cost associated with MCMC presents a considerable challenge, complicating the selection of an appropriate algorithm tailored to the specific problem at hand. This study introduces a novel and comprehensive framework for...
Extreme drought impacts have been underestimated in grasslands and shrublands globally
Melinda D. Smith, Kate D Wilkins, Martin C. Holdrege, Peter A. Wilfahrt, Scott L. Collins, Alan K. Knapp, Osvaldo E. Sala, Jeffrey S. Dukes, Richard P. Phillips, Laura Yahdjian, Laureano A. Gherardi, Timothy Ohlert, Claus Beier, Lauchlan H. Fraser, Anke Jentsch, Michael E. Loik, Fernando T. Maestre, Sally A. Power, Qiang Yu, Andrew J. Felton, Seth M. Munson, Yiqi Luo, Hamed Abdoli, Mehdi Abedi, Concepción L. Alados, Juan Alberti, Moshe Alon, Hui An, Brian Anacker, Maggie Anderson, Harald Auge, Seton Bachle, Khadijeh Bahalkeh, Michael Bahn, Amgaa Batbaatar, Taryn Bauerle, Karen H. Beard, Kai Behn, Ilka Beil, Lucio Biancari, Irmgard Blindow, Viviana Florencia Bondaruk, Elizabeth T. Borer, Edward W. Bork, Carlos Martin Bruschetti, Kerry M. Byrne, James F. Cahill Jr., Dianela A. Calvo, Michele Carbognani, Augusto Cardoni, Cameron N. Carlyle, Miguel Castillo-Garcia, Scott X. Chang, Jeff Chieppa, Marcus V. Cianciaruso, Ofer Cohen, Amanda L. Cordeiro, Daniela F. Cusack, Sven Dahlke, Pedro Daleo, Carla M. D'Antonio, Lee H. Dietterich, Tim S. Doherty, Maren Dubbert, Anne Ebling, Nico Eisenhauer, Felícia M. Fischer, T'ai G. W. Forte, Tobias Gebauer, Beatriz Gozalo, Aaron C. Greenville, Karlo G. Guidoni-Martins, Heather J. Hannusch, Siri Vatsø Haugum, Yann Hautier, Mariet Hefting, Hugh A. L. Henry, Daniela Hoss, Johannes Ingrisch, Oscar Iribarne, Forest Isbell, Yari Johnson, Samuel E. Jordan, Eugene F. Kelly, Kaitlin Kimmel, Juergen Kreyling, György Kröel-Dulay, Alicia Kröpfl, Angelika Kübert, Andrew Kulmatiski, Eric G. Lamb, Klaus Steenberg Larsen, Julie Larson, Jason Lawson, Cintia V. Leder, Anja Linstädter, Jielin Liu, Shirong Liu, Alexandra G. Lodge, Grisel Longo, Alejandro Loydi, Junwei Luan, Frederick Curtis Lubbe, Craig Macfarlane, Kathleen Mackie-Haas, Andrey V. Malyshev, Adrián Maturano-Ruiz, Thomas Merchant, Daniel B. Metcalfe, Akira S. Mori, Edwin Mudongo, Gregory S. Newman, Uffe N. Nielsen, Dale Nimmo, Yujie Niu, Paola Nobre, Rory C. O'Connor, Romà Ogaya, Gastón R. Oñatibia, Ildikó Orbán, Brooke B. Osborne, Rafael Otfinowski, Meelis Pärtel, Josep Penuelas, Pablo L. Peri, Guadalupe Peter, Alessandro Petraglia, Catherine Picon-Cochard, Valério D. Pillar, Juan Manuel Piñeiro-Guerra, Laura W. Ploughe, Robert M. Plowes, Cristy Portales-Reyes, Suzanne M. Prober, Yolanda Pueyo, Sasha C. Reed, Euan G. Ritchie, Dana Aylén Rodríguez, William E. Rogers, Christiane Roscher, Ana M. Sánchez, Bráulio A. Santos, María Cecilia Scarfó, Eric W. Seabloom, Baoku Shu, Lara Souza, Andreas Stampfli, Rachel J. Standish, Marcelo Sternberg, Wei Sun, Marie Sünnemann, Michelle Tedder, Pål Thorvaldsen, Dashuan Tian, Katja Tielbörger, Alejandro Valdecantos, Liesbeth van den Brink, Vigdis Vandvik, Mathew R. Vankoughnett, Liv Guri Velle, Changhui Wang, Yi Wang, Glenda M. Wardle, Christiane Werner, Cunzheng Wei, Georg Wiehl, Jennifer L. Williams, Amelia A. Wolf, Michaela Zeiter, Fawei Zhang, Juntao Zhu, Ning Zong, Xiaoan Zuo
2024, Proceedings of the National Academy of Sciences (121)
Drought has well-documented societal and economic consequences. Climate change is expected to intensify drought to even more extreme levels, but because such droughts have been historically rare, their impact on ecosystem functioning is not well known. We experimentally imposed the most frequent type of intensified drought—one that is ~1 y...
The haunting raptor: Yellowstone’s golden eagles
David B. Haines, Douglas W. Smith, Todd E. Katzner, Victoria J. Dreitz
2023, Book chapter, Yellowstone's Birds- Diversity and Abundance in the World's First National Park
For many who live in North America, when picturing an eagle, the image of a large magnificent bird with a distinct white head and tail comes to mind. Rightfully, the bald eagle has garnered much attention as a national symbol of the United States (US), nearly brought to extinction from...
Integrated science strategy for assessing and monitoring water availability and migratory birds for terminal lakes across the Great Basin, United States
Rebecca J. Frus, Cameron L. Aldridge, Michael L. Casazza, Collin A. Eagles-Smith, Garth Herring, Scott A. Hynek, Daniel K. Jones, Susan K Kemp, Thomas M. Marston, Christopher M. Morris, Ramon C. Naranjo, Cee Nell, David R. O'Leary, Cory T. Overton, Bryce A. Pulver, Brian E. Reichert, Christine A. Rumsey, Rudy Schuster, Cassandra D. Smith
2023, Circular 1516
Executive SummaryIn 2022, the U.S. Geological Survey (USGS) established the Saline Lake Ecosystems Integrated Water Availability Assessment (IWAAs) to monitor and assess the hydrology of terminal lakes in the Great Basin and the migratory birds and other wildlife dependent on those habitats. Scientists from across the USGS (with specialties in...
Influence of a guide net on the presence and behavior of fish near the selective water withdrawal structure in Lake Billy Chinook, Oregon, 2022
Collin D. Smith, Tyson W. Hatton
2023, Open-File Report 2023-1090
Imaging sonar was used to assess the influence of a fish guidance net, installed at the entrances to the selective water withdrawal (SWW) intake structure, in the forebay of Round Butte Dam, Oregon, on behavior, abundance, and timing of fish during the spring of 2022. The purposes of the SWW...
On the relationship between aquatic CO2 concentration and ecosystem fluxes in some of the world’s key wetland types
Jessica L. Richardson, Ankur R. Desai, Jonathon Thom, Kim Lindgren, Hjalmar Laudon, Matthias Peichl, Mats B. Nilsson, Audrey Campeau, Jarvi Jarveoja, Peter Hawman, Deepak R. Mishra, Dontrece Smith, Brenda D'Acunha, Sara H. Knox, Darian Ng, Mark S. Johnson, Joshua M. Blackstock, Sparkle L. Malone, Steve F. Oberbauer, Matteo Detto, Kimberly Wickland, Inke Forbrich, Nathaniel B Weston, Jacqueline K.Y. Hung, Colin W. Edgar, Eugenie S. Euskirchen, Syndonia Bret-Harte, Jason Dobkowski, George Kling, Evan S. Kane, Pascal Badiou, Matthew Bogard, Gil Bohrer, Thomas O'Halloran, Jonny Ritson, Ariane Arias-Otriz, Dennis Baldocchi, Patty Oikawa, Julie Shahan, Maiyah Matsumura
2023, Wetlands (44)
To understand patterns in CO2 partial pressure (PCO2) over time in wetlands’ surface water and porewater, we examined the relationship between PCO2 and land–atmosphere flux of CO2 at the ecosystem scale at 22 Northern Hemisphere wetland sites synthesized through an open call. Sites spanned 6 major wetland types (tidal,...
Unifying the Neoarchean Lac des Iles Complex and implications for the petrogenesis of Pd-enriched noritic breccia pipes in ancient arcs
William D. Smith, L. Fay, M.L. Djon, Michael Jenkins, Y. Lin, Z. S. Yao, James E. Mungall
2023, Conference Paper, 14th International Platinum Symposium abstract volume
No abstract available....
Plant size, latitude, and phylogeny explain within-population variability in herbivory
The Herbivory Variability Network, Moria Robinson, Karen C Abbott, Warwick J. Allen, Janete Andrade, Diego Angulo, Diego Anjos, Daniel Anstett, Robert Bagchi, Sumanta Bagchi, Milton Barbosa, Sarah Barrett, Carina Baskett, Eyal Ben-Simchon, Kathryn Bloodworth, Judith L. Bronstein, Emilio Bruna, Yvonne Buckley, Karin Burghardt, Carlos Bustos-Segura, N. Ivalú Cacho, Eduardo Soares Calixto, Raquel Carvalho, Bastien Castagneyrol, Mariana Chiuffo, Damla Cinoğlu, Elizeth Cinto Mejia, Marina Cock, Rodrigo Cogni, Olivia Cope, Tatiana Cornelissen, Dezirea Cortez, David Crowder, Caroline Dallstream, Wesley Dáttilo, Julien Davis, Romina Dimarco, Haley Dole, Lee Dyer, Ikponmwosa Egbon, Afure Ejomah, Bret D Elderd, María-José Endara, Micky D. Eubanks, Susan Everingham, Keiko Farah, Rafael de Paiva Farias, Geraldo Fernandes, Marco Ferrante, Alain Finn, Grace Florjancic, Matthew L. Forister, Quinn Fox, Enric Frago, Filipe M. França, Abigail Getman-Pickering, Zoe Getman-Pickering, Ben Gooden, Martin M. Gossner, Keri Greig, Sofia Gripenberg, Ronny Groenteman, Patrick Grof-Tisza, Nora Haack, Lisa Hahn, Philip Hahn, Shiekh Marifatul Haq, Justus Hennecke, Sara Hermann, Liza M. Holeski, Matthew Hutchinson, Brian Inouye, Eleanor Jackson, Shinnosuke Kagiya, Michael Kalwajtys, Richard Karban, Rupesh Kariyat, Tamar Keasar, Monica Kersch-Becker, Heather Kharouba, Tania Kim, Duncan Kimuyu, Jennifer Kluse, Sally E. Koerner, Kimberly Komatsu, Sushmita Krishnan, Miika Laihonen, Lucas Lamelas-López, Michael LaScaleia, Nicolas Lecomte, Carlos Lehn, Xiaofei Li, Richard L Lindroth, Eric LoPresti, María Losada, Allison M Louthan, Victoria Luizzi, Joshua Lynn, Nicholas Lyon, Laís Maia, Renata Maia, Tosca Mannall, Bruce Martin, Tara Massad, Andrew McCall, Kelsey McGurrin, Andrew Merwin, Zarluis Mijango-Ramos, Charlotte Mills, Angela Moles, Christopher Moore, Colin Morrison, Moleseng Moshobane, Anne Muola, Ryosuke Nakadai, Kazuhide Nakajima, Samuel Novais, Charlee Ogbebor, Haruna Ohsaki, Vincent Pan, Nicholas Pardikes, Narayanaswamy Parthasarathy, Rohit Pawar, Quentin Paynter, Ian Pearse, Rachel Penczykowski, Adam Pepi, Cássio Pereira, Shyam Phartyal, Frida I. Piper, Katja Poveda, Elizabeth Pringle, Javier Puy, Teresa Quijano, Carolina Quintero, Sergio Rasmann, Christoph Rosche, Leah Rosenheim, Justin B. Runyon, Asaf Sadeh, Yuzu Sakata, Danielle Salcido, Cristian Salgado-Luarte, Bráulio Santos, Yuval Sapir, Yamila Sasal, Yasuhiro Sato, Manasi Sawant, Hayley Schroeder, Isabell Schumann, Michal Segoli, Hila Segre, Oren Shelef, Naoto Shinohara, Rachit Pratap Singh, David Smith, Mar Sobral, Gisela Stotz, Ayco Tack, Mandeep Tayal, John Tooker, Daniel Torrico-Bazoberry, Kévin Tougeron, Nora Underwood, Shunsuke Utsumi, Osariyekemwen Uyi, Jessica Vaca-Uribe, Anu Valtonen, Laura van Dijk, Vigdis Vandvik, Jesus Villellas, Lauren Waller, Marjorie G. Weber, William C. Wetzel, Susan Whitehead, Akira Yamawo, Samantha Yim, Luke Zehr, Zhiwei Zhong
2023, Science (382) 679-683
Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse...
Application of the Stream Salmonid Simulator (S3) model to assess fall Chinook salmon (Oncorhynchus tshawytscha) production in the American River, California
John M. Plumb, Russell W. Perry, Tyson W. Hatton, Collin D. Smith, John M. Hannon
2023, Open-File Report 2023-1060
Executive SummaryAnadromous fish returning to the lower American River are restricted to 36 kilometers of free-flowing river between Nimbus Dam and American River’s confluence with the Sacramento River, California. Salmon in the American River provide an important freshwater recreational fishery. However, annual salmon production in the American River in recent...
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...
Application of the technology readiness levels framework to natural resource management tools
Aaron R. Cupp, Andrea K. Fritts, Marybeth K. Brey, Christa M. Woodley, David Smith, Mark Cornish, Amy McGovern, Rob Simmonds, Neal Jackson
2023, Fisheries (48) 474-479
Technology advancements in fisheries science can provide useful tools to support natural resource management and conservation. However, new technologies may also present challenges for decision makers due to the lack of a standardized process to assess technologies for consideration within management plans. Future technology development in fishery and water resources...
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 (33) 1175-1199
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 (20) 2421-2436
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 (113) 2377-2415
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 (31) 716-738
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 M. 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 (37)
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...
Automatic recorders monitor wolves at rendezvous sites: do wolves adjust howling to live near humans?
Vicente Palacios, Bárbara Martí-Domken, Shannon Barber-Meyer, Bilal Habib, José Vicente López-Bao, Douglas W. Smith, Daniel R. Stahler, Emilio José García, Víctor Sazatornil, L. David Mech
2023, Biodiversity and Conservation (23) 363-383
We used automatic sound recorders to study spontaneous vocalizations of wild wolves during the pup-rearing season around rendezvous sites from 24 wolf packs in six study areas across North America, Asia, and Europe. Between 2018 and 2021, for a total of 1225 pack-days, we recorded 605...
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...
