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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: 42707

Assessments of species' vulnerability to climate change: From pseudo to science Assessments of species' vulnerability to climate change: From pseudo to science

Climate change vulnerability assessments (CCVAs) are important tools to plan for and mitigate potential impacts of climate change. However, CCVAs often lack scientific rigor, which can ultimately lead to poor conservation prioritization and associated ecological and economic costs. We discuss the need to improve comparability and consistency of CCVAs and either validate their findings or...
Authors
Alisa A. Wade, Brian K. Hand, Ryan Kovach, Clint C. Muhlfeld, Robin S. Waples, Gordon Luikart

Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil

Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological...
Authors
Erin E. Silvestri, David Feldhake, Dale Griffin, John T. Lisle, Tonya L. Nichols, Sanjiv Shah, A Pemberton, Frank W Schaefer III

Climate, invasive species and land use drive population dynamics of a cold-water specialist Climate, invasive species and land use drive population dynamics of a cold-water specialist

Climate change is an additional stressor in a complex suite of threats facing freshwater biodiversity, particularly for cold-water fishes. Research addressing the consequences of climate change on cold-water fish has generally focused on temperature limits defining spatial distributions, largely ignoring how climatic variation influences population dynamics in the context of other...
Authors
Ryan P. Kovach, Robert K. Al-Chokhachy, Diane C. Whited, David A. Schmetterling, Andrew M. Dux, Clint C. Muhlfeld

Alternative approaches to vertebrate ecotoxicity tests in the 21st century: A review of developments over the last 2 decades and current status Alternative approaches to vertebrate ecotoxicity tests in the 21st century: A review of developments over the last 2 decades and current status

The need for alternative approaches to the use of vertebrate animals for hazard assessment of chemicals and pollutants has become of increasing importance. It is now the first consideration when initiating a vertebrate ecotoxicity test, to ensure that unnecessary use of vertebrate organisms is minimized wherever possible. For some regulatory purposes, the use of vertebrate organisms for
Authors
Adam Lillicrap, Scott Belanger, Natalie Burden, David Du Pasquier, Michelle Embry, Marlies Halder, Mark Lampi, Lucy Lee, Teresa J. Norberg-King, Barnett A. Rattner, Kristin Schirmer, Paul Thomas

Mitigating amphibian chytridiomycosis in nature Mitigating amphibian chytridiomycosis in nature

Amphibians across the planet face the threat of population decline and extirpation caused by the disease chytridiomycosis. Despite consensus that the fungal pathogens responsible for the disease are conservation issues, strategies to mitigate their impacts in the natural world are, at best, nascent. Reducing risk associated with the movement of amphibians, non-amphibian vectors and other...
Authors
Trenton W. J. Garner, Benedikt R. Schmidt, An Martel, Frank Pasmans, Erin L. Muths, Andrew A. Cunningham, Che Weldon, Matthew C. Fisher, Jaime Bosch

Snake fungal disease: An emerging threat to wild snakes Snake fungal disease: An emerging threat to wild snakes

Since 2006, there has been a marked increase in the number of reports of severe and often fatal fungal skin infections in wild snakes in the eastern USA. The emerging condition, referred to as snake fungal disease (SFD), was initially documented in rattlesnakes, where the infections were believed to pose a risk to the viability of affected populations. The disease is caused...
Authors
Jeffrey M. Lorch, Susan Knowles, Julia S. Lankton, Kathy Michell, Jaime L. Edwards, Joshua M. Kapfer, Richard A. Staffen, Erik R. Wild, Katie Z. Schmidt, Anne Ballmann, Doug Blodgett, Terence M. Farrell, Brad M. Glorioso, Lisa A. Last, Steven J. Price, Krysten L. Schuler, Christopher Smith, James F. X. Wellehan, David S. Blehert

Conserving the Greater Sage-grouse: A social-ecological systems case study from the California-Nevada region Conserving the Greater Sage-grouse: A social-ecological systems case study from the California-Nevada region

The Endangered Species Act (ESA) continues to serve as one of the most powerful and contested federal legislative mandates for conservation. In the midst of heated debates, researchers, policy makers, and conservation practitioners champion the importance of cooperative conservation and social-ecological systems approaches, which forge partnerships at multiple levels and scales to...
Authors
Alison L Duvall, Alexander L. Metcalf, Peter S. Coates

A landscape-scale assessment of above- and belowground primary production in coastal wetlands: Implications for climate change-induced community shifts A landscape-scale assessment of above- and belowground primary production in coastal wetlands: Implications for climate change-induced community shifts

Above- and belowground production in coastal wetlands are important contributors to carbon accumulation and ecosystem sustainability. As sea level rises, we can expect shifts to more salt-tolerant communities, which may alter these ecosystem functions and services. Although the direct influence of salinity on species-level primary production has been documented, we lack an understanding...
Authors
Camille L. Stagg, Donald R. Schoolmaster, Sarai C. Piazza, Gregg Snedden, Gregory D. Steyer, Craig J Fischenich, Robert W. McComas

Extending ordinal regression with a latent zero-augmented beta distribution Extending ordinal regression with a latent zero-augmented beta distribution

Ecological abundance data are often recorded on an ordinal scale in which the lowest category represents species absence. One common example is when plant species cover is visually assessedwithin bounded quadrats and then assigned to pre-defined cover class categories.We present an ordinal beta hurdle model that directly models ordinal category probabilitieswith a biologically realistic...
Authors
Kathryn M. Irvine, T.J. Rodhouse, Ilai. N. Keren

Weak support for disappearance and restricted emergence/persistence of highly pathogenic influenza A in North American waterfowl Weak support for disappearance and restricted emergence/persistence of highly pathogenic influenza A in North American waterfowl

Krauss et al. (1) use lack of detection of highly pathogenic (HP) H5 clade 2.3.4.4 (henceforth "H5") influenza A viruses (IAVs) from >22,000 wild bird samples collected in North America in 2014–2015 to argue that HP H5 IAVs disappeared from waterfowl and that unresolved mechanisms restrict emergence and perpetuation of HP IAVs in natural reservoir species. Here we offer an alternative
Authors
Andrew M. Ramey, Erica Spackman, Mia Kim Torchetti, Thomas J. DeLiberto

Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

Background Adaptive radiation involving a colonizing phenotype that rapidly evolves into at least one other ecological variant, or ecotype, has been observed in a variety of freshwater fishes in post-glacial environments. However, few studies consider how phenotypic traits vary with regard to neutral genetic partitioning along ecological gradients. Here, we present the first detailed...
Authors
Shauna M. Baillie, Andrew M. Muir, Michael J. Hansen, Charles C. Krueger, Paul Bentzen

Statistical correction of lidar-derived digital elevation models with multispectral airborne imagery in tidal marshes Statistical correction of lidar-derived digital elevation models with multispectral airborne imagery in tidal marshes

Airborne light detection and ranging (lidar) is a valuable tool for collecting large amounts of elevation data across large areas; however, the limited ability to penetrate dense vegetation with lidar hinders its usefulness for measuring tidal marsh platforms. Methods to correct lidar elevation data are available, but a reliable method that requires limited field work and maintains...
Authors
Kevin Buffington, Bruce D. Dugger, Karen M. Thorne, John Y. Takekawa
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