Publications
Publications from USGS science centers throughout the Southeast Region.
Filter Total Items: 9949
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the consortium generated over 427 million long-read sequences from complementary DNA and direct RNA datasets, encompassing human, mouse and manatee species. Developers utilized these da
Authors
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E. Loveland, Maite De María, Matthew S. Adams, Gabriela Balderrama-Gutierrez, Amit K. Behera, Jose M. Gonzalez Martinez, Toby Hunt, Julien Lagarde, Cindy E. Liang, Haoran Li, Marcus Jerryd Meade, David A. Moraga Amador, Andrey D. Prjibelski, Inanc Birol, Hamed Bostan, Ashley M. Brooks, Muhammed Hasan Çelik, Ying Chen, Mei R.M. Du, Colette Felton, Jonathan Göke, Saber Hafezqorani, Ralf Herwig, Hideya Kawaji, Joseph Lee, Jian-Liang Li, Matthias Lienhard, Alla Mikheenko, Dennis Mulligan, Ka Ming Nip, Mihaela Pertea, Matthew E. Ritchie, Andre D. Sim, Alison D. Tang, Yuk Kei Wan, Changqing Wang, Brandon Y. Wong, Chen Yang, If Barnes, Andrew E. Berry, Salvador Capella-Gutierrez, Alyssa Cousineau, Namrita Dhillon, Jose M. Fernandez-Gonzalez, Luis Ferrández-Peral, Natàlia Garcia-Reyero, Stefan Götz, Carles Hernández-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomás, Jonathan M. Mudge, Nedka G. Panayotova, Alejandro Paniagua, Dmitry Repchevsky, Xingjie Ren, Eric Rouchka, Brandon Saint-John, Enrique Sapena, Leon Sheynkman, Melissa Laird Smith, Marie-Marthe Suner, Hazuki Takahashi, Ingrid A. Youngworth, Piero Carninci, Nancy D. Denslow, Roderic Guigó, Maggie Hunter, Rene Maehr, Yin Shen, Hagen U. Tilgner, Barbara J. Wold, Christopher Vollmers, Adam Frankish, Kin Fai Au, Gloria M. Sheynkman, Ali Mortazavi, Ana Conesa, Angela N. Brooks
Projected sea-level rise and high tide flooding at Timucuan Ecological and Historic Preserve, Florida
IntroductionNational parks and preserves in the South Atlantic-Gulf Region contain valuable coastal habitats such as tidal wetlands and mangrove forests, as well as irreplaceable historic buildings and archeological sites located in low-lying areas. These natural and cultural resources are vulnerable to accelerated sea-level rise and escalating high tide flooding events. Through a Natural Resource
Authors
Hana R. Thurman, Nicholas M. Enwright, Michael J. Osland, Davina L. Passeri, Richard H. Day, Bethanie M. Simons
Development of high surface area organosilicate nanoparticulate thin films for use in sensing hydrophobic compounds in sediment and water
The scope of this study was to apply advances in materials science, specifically the use of organosilicate nanoparticles as a high surface area platform for passive sampling of chemicals or pre-concentration for active sensing in multiple-phase complex environmental media. We have developed a novel nanoporous organosilicate (NPO) film as an extraction phase and proof of concept for application in
Authors
Sangho Bok, Venumadhav R. Korampally, Jacob K. Stanley, Keshab Gangopadhyay, Shubhra Gangopadhyay, Jeffery Steevens
Enhancing assessments of coastal wetland migration potential with sea-level rise: Accounting for uncertainty in elevation data, tidal data, and future water levels
Sea-level rise rates are predicted to surpass rates of wetland vertical adjustment in the coming decades in many areas, increasing the potential for wetland submergence. Information on where wetland migration is possible can help natural resource managers for planning land acquisition or enhancing habitat connectivity to bolster adaptation of coastal wetlands to rising seas. Elevation-based models
Authors
Nicholas Enwright, Michael Osland, Hana R. Thurman, Claire E. McHenry, William C. Vervaeke, Brett Patton, Davina Passeri, Jason M. Stoker, Richard Day, Bethanie M. Simons
Preparing for today's and tomorrow's water-resources challenges in eastern Long Island, New York
Freshwater is a vital natural resource. Although New York is a water-rich State, the wise and economical use of water resources is needed to ensure that there is enough water of adequate quality for both human and ecological needs—both for today and for tomorrow. Nowhere in New York is this more evident than in Nassau and Suffolk Counties on Long Island, where the public water supply is obtained f
Authors
Ronald Busciolano, John P. Masterson, Robert F. Breault
Deep vs shallow: GPS tags reveal a dichotomy in movement patterns of loggerhead turtles foraging in a coastal bay
BackgroundIndividual variation in movement strategies of foraging loggerhead turtles have been documented on the scale of tens to hundreds of kilometers within single ocean basins. Use of different strategies among individuals may reflect variations in resources, predation pressure or competition. It is less common for individual turtles to use different foraging strategies on the scale of kilomet
Authors
Margaret Lamont, Daniel Slone, James P. Reid, Susan M. Butler, Joseph A. Alday
Impact of Hurricane Irma on coral reef sediment redistribution at Looe Key Reef, Florida, USA
Understanding event-driven sediment transport in coral reef environments is essential to assessing impacts on reef species, habitats, restoration, and mitigation, yet a global knowledge gap remains due to limited quantitative studies. Hurricane Irma made landfall in the Lower Florida Keys with sustained 209 km h−1 winds and waves greater than 8 m on 10 September 2017, directly impacting the Florid
Authors
Kimberly Yates, Zachery Fehr, Selena Anne-Marie Johnson, David G. Zawada
Best practices for genetic and genomic data archiving
Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics
Authors
Deborah M. Leigh, A. G. Vandergast, Maggie Hunter, Eric D. Crandall, W. Chris Funk, Colin J Garroway, Sean M. Hoban, Sara J. Oyler-McCance, Christian Rellstab, Gernot Segelbacher, Chloe Schmidt, Ella Vázquez-Domínguez, Ivan Paz-Vinas
Environmental DNA
The widespread adoption of environmental DNA (eDNA) detection tools for biodiversity monitoring has led to the need for universal data standards to inform principled eDNA data applications. Improvements in understanding the meaning and possible uncertainty of eDNA data can minimize erroneous conclusions, increase confidence in eDNA data, and maximize conservation outcomes.
-Environmental DNA (eDN
Authors
Maggie Hunter, Kristian Meissner, Catherine Abbott, Florien Leese, Gernot Segelbacher
Interdisciplinary science approach for harmful algal blooms (HABs) and algal toxins—A strategic science vision for the U.S. Geological Survey
Executive SummaryAlgal blooms in water, soils, dusts, and the environment have captured national attention because of concerns associated with exposure to algal toxins for humans and animals. Algal blooms naturally occur in all surface-water types and are important primary producers for aquatic ecosystems. However, excessive algae growth can be associated with many harmful effects ranging from aes
Authors
Victoria G. Christensen, Christopher J. Crawford, Robert J. Dusek, Michael J. Focazio, Lisa Reynolds Fogarty, Jennifer L. Graham, Celeste A. Journey, Mari E. Lee, James H. Larson, Sarah M. Stackpoole, Viviana Mazzei, Emily J. Pindilli, Barnett A. Rattner, E. Terrence Slonecker, Kristen B. McSwain, Timothy J. Reilly, Ashley E. Lopez
By
Ecosystems Mission Area, Water Resources Mission Area, Environmental Health Program, Toxic Substances Hydrology, Earth Resources Observation and Science (EROS) Center , Kansas Water Science Center, National Wildlife Health Center, New Jersey Water Science Center, New York Water Science Center, South Atlantic Water Science Center (SAWSC), Upper Midwest Water Science Center, Landsat Missions
Capturing potential: Leveraging grass carp behavior Ctenopharyngodon idella for enhanced removal
Effective management of invasive species benefits from a comprehensive understanding of the species’ behavior and interactions with the invaded system. We investigated temporal dynamics of telemetry detections and the potential utility of a traitor approach for informing response efforts to the invasive grass carp (Ctenopharyngodon idella) population in the Sandusky River, a major tributary to Lak
Authors
Matthew Ross Acre, Tyler Michael Hessler, Sophia Marie Bonjour, James Roberts, Scott F. Colborne, Travis O. Brenden, Lucas R. Nathan, Dustin Broaddus, Christopher S. Vandergoot, Christine M. Mayer, Song S. Qian, Robert D. Hunter, Ryan E. Brown, Robin Calfee
Magnitude and frequency of floods in the Coastal Plain region of Louisiana, 2016
To improve flood-frequency estimates for rural streams in the Coastal Plain region of Louisiana, generalized least-squares regression techniques were used to relate corresponding annual exceedance probability streamflows for 211 streamgages in the region to a suite of explanatory variables that include physical, climatic, pedologic, and land-use characteristics of the streamgage drainage area. The
Authors
Paul A. Ensminger, Daniel M. Wagner, Amanda Whaling