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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: 41763

Climate matching with the climatchR R package

Climate matching allows comparisons of climatic conditions between different locations to understand location and species range climatic suitability. The approach may be used as part of horizon scanning exercises such as those conducted for invasive species. We implemented the CLIMATCH algorithm into an R package, climatchR. The package allows automated and scripted climate matching exercises acro
Authors
Richard A. Erickson, Peder S Engelstad, Catherine S. Jarnevich, Helen Sofaer, Wesley M. Daniel

The influence of satellite-derived environmental and oceanographic parameters on marine turtle time at surface in the Gulf of Mexico

The aftermath of the 2010 Deepwater Horizon oil spill highlighted the lack of baseline spatial, behavioral, and abundance data for many species, including imperiled marine turtles, across the Gulf of Mexico. The ecology of marine turtles is closely tied to their vertical movements within the water column and is therefore critical knowledge for resource management in a changing ocean. A more compre
Authors
Kelsey E. Roberts, Lance P. Garrison, Joel G. Ortega-Ortiz, Chuanmin Hu, Yingjun Zhang, Christopher R. Sasso, Margaret Lamont, Kristen Hart

Development of a ddPCR assay for the detection of the Smoky Madtom (Noturus baileyi) from eDNA in stream water samples

The Smoky Madtom Noturus baileyi is a federally endangered species, whose native distribution includes lower Abrams Creek in Great Smoky Mountains National Park (GRSM) and Citico Creek in nearby Cherokee National Forest. Due to challenges for bio-monitoring posed by its nocturnality and cryptic life history, an environmental DNA (eDNA)-based approach for detection would be useful to complement exi
Authors
Aaron Aunins, Michael S. Eackles, Paul E Super, Matt A. Kulp, Becky J Nichols, Barbara A. Lubinski, Cheryl L. Morrison, Timothy L. King

Using ecosystem services to identify inequitable outcomes in migratory species conservation

Biodiversity conservation efforts have been criticized for generating inequitable socio-economic outcomes. These equity challenges are largely analyzed as place-based problems affecting local communities directly impacted by conservation programs. The conservation of migratory species extends this problem geographically since people in one place may benefit while those in another bear the costs of
Authors
Charles C. Chester, Aaron M. Lien, Juanita Sundberg, James E. Diffendorfer, Columba Gonzales, Brady J. Mattsson, Rodrigo Medellin, Darius J. Semmens, Wayne E. Thogmartin, Jonathan J. Derbridge, Laura López-Hoffman

Hydrologic connectivity and residence time affect the sediment trapping efficiency and dissolved oxygen concentrations of the Atchafalaya River Basin

Little is known about water movement, volume, or residence time (RT), and how those characteristics affect sediment trapping efficiency (TE) and dissolved oxygen concentrations (DO) in the United States' largest remaining bottomland hardwood swamp, the Atchafalaya River Basin. To better understand these dynamics, this study used bathymetry, lidar, and stage records to determine volumes in the Basi
Authors
Daniel Kroes, Richard Day, Michael D. Kaller, Charles R. Demas, William E. Kelso, Tiffany Pasco, Raynie Harlan, Steven Roberts

Rapid SNP genotyping, sex identification, and hybrid-detection in threatened bull trout

We developed new bull trout genetic markers using Restriction-site Associated DNA sequencing (RAD-seq) to improve our ability to address questions important for their conservation and management. Samples from across the species range were sequenced and 5020 high quality single nucleotide polymorphism (SNP) loci were discovered, including hundreds with high heterozygosity (H > 0.30). We developed 6
Authors
Stephen J. Amish, Shana Bernall, Patrick W. DeHaan, Michael A. Miller, Sean M. O'Rourke, Matthew Boyer, Clint C. Muhlfeld, Angela Lodmell, Robb F. Leary, Gordon Luikart

Avian influenza antibody prevalence increases with mercury contamination in wild waterfowl

Environmental contamination is widespread and can negatively impact wildlife health. Some contaminants, including heavy metals, have immunosuppressive effects, but prior studies have rarely measured contamination and disease simultaneously, which limits our understanding of how contaminants and pathogens interact to influence wildlife health. Here, we measured mercury concentrations, influenza inf
Authors
Claire Stewart Teitelbaum, Josh T. Ackerman, Mason A. Hill, Jaqueline M. Satter, Michael L. Casazza, Susan E. W. De La Cruz, Walter M. Boyce, Evan James Buck, John M. Eadie, Mark P. Herzog, Elliott Matchett, Cory T. Overton, Sarah H. Peterson, Magdalena Plancarte, Andrew M. Ramey, Jeffery D. Sullivan, Diann Prosser

Direct and indirect influences of macrophyte cover on abundance and growth of juvenile Atlantic salmon

1. The relationships between macrophytes and the physical and biological characteristics of the environments that aquatic organisms inhabit are complex. Previous studies have shown that the macrophytes, Ranunculus (subgenus Batrachium), which are dominant in lowland chalk streams and widespread across Europe, can enhance juvenile Atlantic salmon abundance and growth to a greater degree than other
Authors
Jessica E Marsh, J. Iwan Jones, Rasmus B. Lauridsen, James Grace, Pavel Kratina

Social effects of rabies infection in male vampire bats (Desmodus rotundus)

Rabies virus (RABV) transmitted by the common vampire bat (Desmodus rotundus) poses a threat to agricultural development and public health throughout the Neotropics. The ecology and evolution of rabies host-pathogen dynamics are influenced by two infection-induced behavioral changes. RABV-infected hosts often exhibit increased aggression which facilitates transmission, and rabies also leads to red
Authors
Elsa M. Cárdenas-Canales, Sebastian Stockmaier, Eleanor Cronin, Tonie E. Rocke, Jorge E. Osorio, Gerald G. Carter

Landscape genetics of a sub-alpine toad: Climate change predicted to induce upward range shifts via asymmetrical migration corridors

Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations,
Authors
Paul A. Maier, A. G. Vandergast, Steven M Ostoja, Andres Aguilar, Andrew J. Bohonak

Monitoring framework to evaluate effectiveness of aquatic and floodplain habitat restoration activities for native fish along the Willamette River, northwestern Oregon

Since 2008, large-scale restoration programs have been implemented along the Willamette River, Oregon, to address historical losses of floodplain habitats caused by dam construction, bank protection, large wood removal, land conversion, and other anthropogenic influences. The Willamette Focused Investment Partnership (WFIP) restoration initiative brings together more than 16 organizations to impro
Authors
Mackenzie K. Keith, J. Rose Wallick, Rebecca L. Flitcroft, Tobias J. Kock, Laura A. Brown, Rich Miller, Joan C. Hagar, Kathleen Guillozet, Krista L. Jones

Socioeconomic resilience to climatic extremes in a freshwater fishery

Heterogeneity is a central feature of ecosystem resilience, but how this translates to socioeconomic resilience depends on people’s ability to track shifting resources in space and time. Here, we quantify how climatic extremes have influenced how people (fishers) track economically valuable ecosystem services (fishing opportunities) across a range of spatial scales in rivers of the northern Rocky
Authors
Timothy Joseph Cline, Clint C. Muhlfeld, Ryan P. Kovach, Robert Al-Chokhachy, David Schmetterling, Diane Whited, Abigail Lynch