Publications
This list of publications includes peer-review journal articles, official USGS publications series, reports and more authored by scientists in the Ecosystems Mission Area. A database of all USGS publications, with advanced search features, can be accessed at the USGS Publications Warehouse.
Filter Total Items: 42912
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification 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...
Authors
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, Mark Diekhans, Silvia 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 Celik, Ying Chen, Mei R.M. Du, Colette Felton, Jonathan Goke, 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 Ferrandez-Peral, Natàlia Garcia-Reyero, Stefan Gotz, Carles Hernandez-Ferrer, Liudmyla Kondratova, Tianyuan Liu, Alessandra Martinez-Martin, Carlos Menor, Jorge Mestre-Tomas, 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 Guigo, Margaret 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
Bornean Wren-Babbler Ptilocichla leucogrammica Bornean Wren-Babbler Ptilocichla leucogrammica
No abstract available.
Authors
Ryan C. Burner, Guy M. Kirwan, Peter Pyle, Nigel J. Collar, Craig Robson
Bare-headed Laughingthrush Melanocichla calva Bare-headed Laughingthrush Melanocichla calva
No abstract available.
Authors
Ryan C. Burner, Guy M. Kirwan, Peter Pyle, Nigel J. Collar, Craig Robson
Hirsutonosema embarrassi n. gen. n. sp. (Phylum Microsporidia) in the Ovary of Mucket (Actinonaias ligamentina), Plain Pocketbook (Lampsilis cardium), and Fatmucket (Lampsilis siliquoidea) (Unionidae) from the Embarrass River, Wisconsin, USA Hirsutonosema embarrassi n. gen. n. sp. (Phylum Microsporidia) in the Ovary of Mucket (Actinonaias ligamentina), Plain Pocketbook (Lampsilis cardium), and Fatmucket (Lampsilis siliquoidea) (Unionidae) from the Embarrass River, Wisconsin, USA
During an epidemiological survey following a mortality event of freshwater mussels in 2018 in the Embarrass River, Wisconsin, USA, we identified a novel microsporidian parasite in the ovaries of mucket (Actinonaias ligamentina), plain pocketbook (Lampsilis cardium), and fatmucket (Lampsilis siliquoidea) (Unionidae). Histopathology showed round-to-oval microsporidian spores in the...
Authors
Susan Knowles, Eric M. Leis, J.C. Richard, I.F. Standish, Jamie Bojko, Jesse Weinzinger, Diane L. Waller
Fish invasion of prairie pothole wetlands reduces amphipod abundance, a key vertebrate forage Fish invasion of prairie pothole wetlands reduces amphipod abundance, a key vertebrate forage
Fishes have spread into previously fishless wetlands, likely affecting other species. In the Prairie Pothole Region of North America, the invasion of fish into wetlands is facilitated by interactions of altered land use, climate, and hydrology. We aimed to understand the effects of fishes on amphipods, which are macroinvertebrates that vertebrates rely on as forage. We hypothesized the...
Authors
Jake D. Carleen, Danelle M. Larson, Michael J. Anteau, Megan J. Fitzpatrick, Andrew W. Hafs, Carl W. Isaacson, Breanna R. Keith
Climate-influenced phenology of larval fish transport in a large lake Climate-influenced phenology of larval fish transport in a large lake
Elucidating physical transport phenologies in large lakes can aid understanding of larval recruitment dynamics. Here, we integrate a series of climate, hydrodynamic, biogeochemical, and Lagrangian particle dispersion models to: (1) simulate hatch and transport of fish larvae throughout an illustrative large lake, (2) evaluate patterns of historic and potential future climate-induced...
Authors
Spencer T. Gardner, Mark D. Rowe, Pengfei Xue, Xing Zhou, Peter Alsip, David Bunnell, Paris D. Collingsworth, Edward S. Rutherford, Tomas O. Hook
Bird community response to one decade of riparian restoration along the Colorado River delta in Mexico Bird community response to one decade of riparian restoration along the Colorado River delta in Mexico
We assessed the response of breeding birds to one decade of riparian restoration in the Colorado River delta including active vegetation management since 2010 and various environmental water deliveries since 2014. Bird surveys were conducted from 2002 to 2021 at 230 bird count stations distributed along five river reaches with different hydrogeomorphic characteristics, across 7 routes in...
Authors
Eduardo Gonzalez-Sargas, Timothy D Meehan, Osvel Hinojosa-Huerta, Steffany Villagomez-Palma, Alejandra Calvo-Fonseca, Christopher Dodge, Martha Gomez-Sapiens, Patrick B. Shafroth
Change in growth and prey utilization for a native salmonid following invasion by an omnivorous minnow in an oligotrophic reservoir Change in growth and prey utilization for a native salmonid following invasion by an omnivorous minnow in an oligotrophic reservoir
Aquatic invasive species can affect food web structure, native fish growth, and production, depending on the traits of the invasive species and the pre-invasion conditions of the ecosystem. Thermal tolerances and behavioral traits can further influence differential exploitation of resources shared between native and invasive species. An unauthorized introduction of redside shiner...
Authors
Rachelle Carina Johnson, Tessa Julianne Code, Karl D. Stenberg, Jonathan H Mclean, Benjamin Lorenz Jensen, Marshal S. Hoy, David Beauchamp
Projected sea-level rise and high tide flooding at Timucuan Ecological and Historic Preserve, Florida Projected sea-level rise and high tide flooding at Timucuan Ecological and Historic Preserve, Florida
Introduction National 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...
Authors
Hana R. Thurman, Nicholas M. Enwright, Michael J. Osland, Davina L. Passeri, Richard H. Day, Bethanie M. Simons
Valuing wildlife sightings at the species-wide and individual animal levels: An approach and application to bear viewing in Yellowstone National Park Valuing wildlife sightings at the species-wide and individual animal levels: An approach and application to bear viewing in Yellowstone National Park
Wildlife viewing is a popular recreation activity in parks and protected areas around the world, yet information on the nonmarket value that visitors derive from viewing specific species, and how that value is affected by small-scale population changes, is lacking. We devised an approach to fill the gap. First, we applied the travel cost method to obtain the value of a wildlife viewing...
Authors
Leslie Richardson, Aaron Joey Enriquez
Development of high surface area organosilicate nanoparticulate thin films for use in sensing hydrophobic compounds in sediment and water 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...
Authors
Sangho Bok, Venumadhav R. Korampally, Jacob K. Stanley, Keshab Gangopadhyay, Shubhra Gangopadhyay, Jeffery A. Steevens
Avian communities respond to plant and landscape composition in actively revegetated floodplains of the Colorado River delta in Mexico Avian communities respond to plant and landscape composition in actively revegetated floodplains of the Colorado River delta in Mexico
We examined the influence of local habitat factors such as plant community composition and species cover, and landscape habitat factors (e.g., land cover types) on the composition of the avian community in an arid-region large river delta (Colorado River). This 106 river km-long study area has experienced restoration through environmental water deliveries and active management of...
Authors
Eduardo Gonzalez-Sargas, Martha Gomez-Sapiens, Osvel Hinojosa-Huera, Steffany Villagomez-Palma, Alejandra Calvo-Fonseca, Joanna Grand, Timothy D. Meehan, Christopher Dodge, Pamela L. Nagler, Carlos Restrepo-Giraldo, Carlos Nieblas, Angela Melendez, Roberto Real Rangel, Patrick B. Shafroth