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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: 42702

The evolution of a tropical biodiversity hotspot The evolution of a tropical biodiversity hotspot

The role of the environment in the origin of new species has long been debated. Harvey et al.examined the evolutionary history and species diversity of suboscine birds in the tropics (see the Perspective by Morlon). Contrary to expectations that the tropics have higher rates of speciation, the authors observed that higher and more constant speciation rates occur in harsh environments...
Authors
Michael G Harvey, Gustavo A Bravo, Santiago Claramunt, Andres M Cuervo, Graham E Derryberry, Jaqueline Battilana, Glenn F Seeholzer, Jessica Shearer McKay, Brian C. O’Meara, Brant C Faircloth, Scott V Edwards, Jorge Perez-Eman, Robert G Moyle, Frederick H. Sheldon, Alexandre Aleixo, Brian T Smith, Terry Chesser, Luis F Silveira, Joel Cracraft, Robb T Brumfield, Elizabeth P Derryberry

Resist-accept-direct (RAD)-A framework for the 21st-century natural resource manager Resist-accept-direct (RAD)-A framework for the 21st-century natural resource manager

An assumption of stationarity—i.e. “the idea that natural systems fluctuate within an unchanging envelope of variability” (Milly et al. 2008)—underlies traditional conservation and natural resource management, as evidenced by widespread reliance on ecological baselines to guide protection, restoration, and other management. Although ecological change certainly occurred under the...
Authors
Gregor W. Schuurman, Cat Hawkins Hoffman, David N. Cole, David J. Lawrence, John M. Morton, Dawn R. Magness, Amanda E. Cravens, Scott Covington, Robin O'Malley, Nicholas A. Fisichelli

Predator and prey events at the entrance of a surface‐oriented fish collector at North Fork Dam, Oregon Predator and prey events at the entrance of a surface‐oriented fish collector at North Fork Dam, Oregon

Quantifiable estimates of predator–prey interactions and relationships in aquatic habitats are difficult to obtain and rare, especially when individuals cannot be readily observed. To overcome this observational impediment, imaging sonar was used to assess the cooccurrence of predator‐size fish and juvenile salmonids, Oncorhynchus spp., at the entrance to a floating surface collector...
Authors
Collin Smith, John Plumb, Noah S. Adams, Garth J Wyatt

Comparing methods to estimate the proportion of turbine-induced bird and bat mortality in the search area under a road and pad search protocol Comparing methods to estimate the proportion of turbine-induced bird and bat mortality in the search area under a road and pad search protocol

Estimating bird and bat mortality at wind facilities typically involves searching for carcasses on the ground near turbines. Some fraction of carcasses inevitably lie outside the search plots, and accurate mortality estimation requires accounting for those carcasses using models to extrapolate from searched to unsearched areas. Such models should account for variation in carcass density...
Authors
Joseph Maurer, Manuela Huso, Daniel Dalthorp, Lisa Madsen, Claudio Fuentes

Climate and Ecological Disturbance Analysis of Engelmann spruce and Douglas fir in the Greater Yellowstone Ecosystem Climate and Ecological Disturbance Analysis of Engelmann spruce and Douglas fir in the Greater Yellowstone Ecosystem

The effects of anthropogenic climate change are apparent in the Greater Yellowstone Ecosystem (GYE), USA, with forest die-off, insect outbreaks, and wildfires impacting forest ecosystems. A long-term perspective would enable assessment of the historical range of variability in forest ecosystems and better determination of recent forest dynamics and historical thresholds. The objectives...
Authors
Brittany Rinaldi, R. Stockton Maxwell, Thomas Callahan, Rebecca Lynn Brice, Karen Heeter, Grant L. Harley

Assessment of two techniques for remediation of lacustrine rocky reef spawning habitat Assessment of two techniques for remediation of lacustrine rocky reef spawning habitat

Rocky reef habitats in lacustrine systems constitute important areas for lithophilic‐spawning fishes. Interstitial spaces created by the structure of rocky reefs form microenvironments where incubating embryos and juvenile fish are potentially protected from predators and physical displacement. However, if interstitial spaces are filled or blocked by sediment or biofouling, the reef...
Authors
Alex Gatch, S.K. Koenigbauer, Edward F. Roseman, T. Hook

Systematics, evolution, and genetics of bears Systematics, evolution, and genetics of bears

Molecular genetics are key to understanding current and historical relationships between isolated populations, including species’ colonizations during glacial–interglacial cycles, to determine viability of local populations, needs for habitat corridors, and other aspects of population management, especially where bears are harvested for sport, etc. As natural habitats shrink, some bear...
Authors
Andrew C Kitchener, Eva Bellemain, Xiang Ding, Alexander Kopatz, Verena Kutschera, Valentina Salomashkina, Manuel Ruiz-Garcia, Tabitha A. Graves, Yiling Hou, Lars Werdelin, Axel Janke

Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management Characterizing patterns of genomic variation in the threatened Utah prairie dog: Implications for conservation and management

Utah prairie dogs (Cynomys parvidens) are federally threatened due to eradication campaigns, habitat destruction, and outbreaks of plague. Today, Utah prairie dogs exist in small, isolated populations, making them less demographically stable and more susceptible to erosion of genetic variation by genetic drift. We characterized patterns of genetic structure at neutral and putatively...
Authors
Rachel M. Giglio, Tonie E. Rocke, Jorge E. Osorio, Emily K. Latch

Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes salmonids Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes salmonids

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle...
Authors
Katherine Eaton, Moises Bernal, Nathan Backenstose, Daniel Yule, Trevor J. Krabbenhoft

Conservation genomics of the threatened western spadefoot, Spea hammondii, in urbanized southern California Conservation genomics of the threatened western spadefoot, Spea hammondii, in urbanized southern California

Populations of the western spadefoot (Spea hammondii) in southern California occur in one of the most urbanized and fragmented landscapes on the planet and have lost up to 80% of their native habitat. Orange County is one of the last strongholds for this pond-breeding amphibian in the region, and ongoing restoration efforts targeting S. hammondii have involved habitat protection and the
Authors
Kevin M Neal, Robert N. Fisher, Milan J. Mitrovich, H. Bradley Shaffer

Evidence of spawning by lake trout Salvelinus namaycush on substrates at the base of large boulders in northern Lake Huron Evidence of spawning by lake trout Salvelinus namaycush on substrates at the base of large boulders in northern Lake Huron

Identification of lake trout spawning sites has focused on cobble substrates associated with bathymetric relief (e.g., ‘contour’ or ‘slope’ along reefs), but this ‘model’ may be narrow in scope. Previous telemetry work conducted near Drummond Island, USA, Lake Huron, identified egg presence in substrates at the base of large boulders (>1 m diameter); however, the extent of this...
Authors
Steve A. Farha, Thomas Binder, Charles R. Bronte, Daniel B. Hayes, John Janssen, J. Ellen Marsden, Stephen Riley, Charles C. Krueger

Optimal sampling design for spatial capture‐recapture Optimal sampling design for spatial capture‐recapture

Spatial capture‐recapture (SCR) has emerged as the industry standard for estimating population density by leveraging information from spatial locations of repeat encounters of individuals. The precision of density estimates depends fundamentally on the number and spatial configuration of traps. Despite this knowledge, existing sampling design recommendations are heuristic and their...
Authors
Gates Dupont, J. Andrew Royle, Muhammad Ali Nawaz, Chris Sutherland
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