Publications
Explore WARC's science publications.
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A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida) A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)
The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast and easily applied strategy for phylogenetic inference of non-model organisms. However, several existing target capture processing pipelines are incapable of incorporating whole genome sequencing (WGS). Here, we develop a new...
Authors
André Gomes-dos-Santos, Elsa Froufe, John M. Pfeiffer, Nathan Johnson, Chase H. Smith, Andre M. Machado, L. Filipe C. Castro, Van Tu Do, Akimasa Hattori, Nicole Garrison, Nathan V. Whelan, Ivan N. Bolotov, Ilya V. Vikhrev, Alexander V. Kondakov, Mohamed Ghamizi, Vincent Prie, Arthur E. Bogan, Manuel Lopes Lima
Quantifying uncertainty in coastal salinity regime for biological application using quantile regression Quantifying uncertainty in coastal salinity regime for biological application using quantile regression
Salinity regimes in coastal ecosystems are highly dynamic and driven by complex geomorphic and hydrological processes. Estuarine biota are generally adapted to salinity fluctuation, but are vulnerable to salinity extremes. Characterizing coastal salinity regime for ecological studies therefore requires representing extremes of salinity ranges at time scales relevant to ecology (e.g...
Authors
Simeon Yurek, Micheal S Allen, Mitchell J. Eaton, David Chagaris, Nathan Reaver, Julien Martin, Peter C Frederick, Mark Dehaven
Modeling impacts of saltwater intrusion on methane and nitrous oxide emissions in tidal forested wetlands Modeling impacts of saltwater intrusion on methane and nitrous oxide emissions in tidal forested wetlands
Emissions of methane (CH4) and nitrous oxide (N2O) from soils to the atmosphere can offset the benefits of carbon sequestration for climate change mitigation. While past study has suggested that both CH4 and N2O emissions from tidal freshwater forested wetlands (TFFW) are generally low, the impacts of coastal droughts and drought-induced saltwater intrusion on CH4 and N2O emissions...
Authors
Hongqing Wang, Zhaohua Dai, Ken Krauss, Carl C. Trettin, Gregory E. Noe, Andrew J. Burton, Eric Ward
Community for data integration 2019 project report Community for data integration 2019 project report
The U.S. Geological Survey Community for Data Integration annually supports small projects focusing on data integration for interdisciplinary research, innovative data management, and demonstration of new technologies. This report provides a summary of the 14 projects supported in fiscal year 2019 and outlines their goals, activities, and accomplishments. Proposals in 2019 were...
Authors
Amanda N. Liford, Caitlin M. Andrews, Aparna Bamzai-Dodson, Joseph A. Bard, David S. Blehert, John B. Bradford, Wesley M. Daniel, Sara L. Caldwell Eldridge, Frank L. Engel, Jason A. Ferrante, Amy K. Gilmer, Margaret E. Hunter, Jeanne M. Jones, Benjamin Letcher, Frances L. Lightsom, Richard R. McDonald, Leah E. Morgan, Sasha C. Reed, Leslie Hsu
By
Ecosystems Mission Area, Water Resources Mission Area, Science Synthesis, Analysis, and Research Program, Science Analytics and Synthesis (SAS), Volcano Hazards Program, Community for Data Integration (CDI), Geology, Geophysics, and Geochemistry Science Center, Geosciences and Environmental Change Science Center, National Wildlife Health Center, Oklahoma-Texas Water Science Center, Southwest Biological Science Center, Volcano Science Center, Western Geographic Science Center, Wetland and Aquatic Research Center , Woods Hole Coastal and Marine Science Center, Science Data Management
Monitoring of wave, current, and sediment dynamics along the Chincoteague living shoreline, Virginia Monitoring of wave, current, and sediment dynamics along the Chincoteague living shoreline, Virginia
Nature-based features, also called living shorelines, are increasingly applied in coastal protection and restoration. However, the processes and mechanisms (feedbacks and interactions) of wave attenuation, current velocity change, and sediment deposition and erosion along the living shoreline remain unclear, thus limiting the adaptive management of living shoreline restoration projects...
Authors
Hongqing Wang, Q. Chen, Nan Wang, William D. Capurso, L.M. Niemoczynski, Ling Zhu, Gregg A. Snedden, Kevin S. Holcomb, Bowdoin W. Lusk, Carol W. Wilson, Sean R. Cornell
Assessing risk communication in the pet and aquarium trade: An analysis of outreach and engagement efforts Assessing risk communication in the pet and aquarium trade: An analysis of outreach and engagement efforts
The international pet and aquarium trade, and intentional or unintentional release of those pets by individuals, has contributed to the establishment of many species to areas where they are not native, resulting in detrimental consequences to local ecosystems, economies, and livelihoods. A number of outreach campaigns across the United States aim to communicate the risk of non-native pet...
Authors
Kelly G. Guilbeau, Kristen Reaver, Blake Blaskowski, Emily Marie Dean, Wesley Daniel
Shorebird monitoring using spatially explicit occupancy and abundance Shorebird monitoring using spatially explicit occupancy and abundance
Loss of habitat and human disturbance are major factors in the worldwide decline of shorebird populations, including that of the threatened migratory piping plover (Charadrius melodus). From 2013 to 2018, we conducted land-based surveys of the shorebird community every other week during the peak piping plover season (September to March). We assessed the ability of a thin plate spline...
Authors
Eve Bohnett, Jessica Schulz, Robert C. Dobbs, Thomas Hoctor, Dave Hulse, Bilal Ahmad, Wajid Rashid, Hardin Waddle
How do ambient conditions and management actions affect manatee movements and habitat use? How do ambient conditions and management actions affect manatee movements and habitat use?
Kings Bay in northwest Florida, USA, is an important winter home of the largest aggregation of Florida manatee (Trichechus manatus latirostris), and the only location in the United States where visitors legally swim and interact with manatees. In addition to ambient conditions, visitors to the area and management actions have the potential to influence manatee behaviors. We tracked 32...
Authors
Daniel Slone, Susan M. Butler, James P. Reid, Joyce Kleen, Joyce Palmer
Hidden in the hills: Phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species Hidden in the hills: Phylogeny of the freshwater mussel genus Alasmidonta (Bivalvia: Unionidae) and description of a new species
Inaccurate taxonomy can lead to species in need of conservation being overlooked, which makes revisionary systematics crucially important for imperilled groups. The freshwater mussel genus Alasmidonta is one such group in need of study. Here, we take a multilocus phylogenetic approach to assess species-level taxonomy of Alasmidonta and test monophyly of this genus. Phylogenetic inference...
Authors
Nathan V. Whelan, Nathan Johnson, Ashantye’ S. Williams, Michael A. Perkins, Caitlin E. Beaver, Jason W. Mays
Nocturnal basking in freshwater turtles: A global assessment Nocturnal basking in freshwater turtles: A global assessment
Diurnal basking (“sunning”) is common in many ectotherms and is generally thought to be a behavioural mechanism for thermoregulation. Recent studies have reported the occurrence of nocturnal basking in a few distantly-related species of freshwater turtles, but the true extent of this behaviour is unknown, and it may be underreported due to sampling biases (e.g., not surveying for turtles...
Authors
Donald T. McKnight, Kendall Ard, Renoir J. Auguste, Gaurav Barhadiya, Michael F. Benard, Paige Boban, Martin L. Dillon, Colleen T. Downs, Brett Alexander DeGregorio, Brad Glorioso, Rachel M. Goodman, Coen Hird, Ethan C. Hollender, Malcolm Kennedy, Rosie A. Kidman, Andrhea Massey, Pearson McGovern, Max Muhlenhaupt, Kayhan Ostovar, Danusia Podgorski, Cormac Price, Beth A. Reinke, Louise M. Streeting, Jane Venezia, Jeanne Young, Eric J. Nordberg
The Everglades vulnerability analysis: Linking ecological models to support ecosystem restoration The Everglades vulnerability analysis: Linking ecological models to support ecosystem restoration
Understanding of the Everglades’ ecological vulnerabilities and restoration needs has advanced over the past decade but has not been applied in an integrated manner. To address this need, we developed the Everglades Vulnerability Analysis (EVA), a decision support tool that uses modular Bayesian networks to predict the ecological outcomes of a subset of the ecosystem’s health indicators...
Authors
Laura D’Acunto, Leonard G. Pearlstine, Saira M. Haider, Caitlin E. Hackett, Dilip Shinde, Stephanie Romanach
Fusing geophysical and remotely sensed data for observing overwash occurrence, frequency, and impact Fusing geophysical and remotely sensed data for observing overwash occurrence, frequency, and impact
Overwash is an important process that enables a barrier island to migrate landward to adapt to rising sea levels but can also impact vegetated areas and create coastal hazards for populated barrier islands. Our overall objectives were to hindcast overwash events from September 2008 to November 2009 and assess whether overwash impacts could be detected using moderate-resolution imagery...
Authors
Nicholas Enwright, P. Soupy Dalyander, Robert L Jenkins, Elizabeth S. Godsey, Spencer J. Stelly