Advanced hierarchical distance sampling
J. Andrew Royle
2016, Book chapter
In this chapter, we cover a number of important extensions of the basic hierarchical distance-sampling (HDS) framework from Chapter 8. First, we discuss the inclusion of “individual covariates,” such as group size, in the HDS model. This is important in many surveys where animals form natural groups that are the...
Estimating abundance
Chris Sutherland, J. Andrew Royle
2016, Book chapter, Reptile ecology and conservation: A handbook of techniques
This chapter provides a non-technical overview of ‘closed population capture–recapture’ models, a class of well-established models that are widely applied in ecology, such as removal sampling, covariate models, and distance sampling. These methods are regularly adopted for studies of reptiles, in order to estimate abundance from counts of marked individuals...
What are hierarchical models and how do we analyze them?
J. Andrew Royle
2016, Book chapter
In this chapter we provide a basic definition of hierarchical models and introduce the two canonical hierarchical models in this book: site occupancy and N-mixture models. The former is a hierarchical extension of logistic regression and the latter is a hierarchical extension of Poisson regression. We introduce basic concepts of...
Modeling abundance using multinomial N-mixture models
J. Andrew Royle
2016, Book chapter
Multinomial N-mixture models are a generalization of the binomial N-mixture models described in Chapter 6 to allow for more complex and informative sampling protocols beyond simple counts. Many commonly used protocols such as multiple observer sampling, removal sampling, and capture-recapture produce a multivariate count frequency that has a multinomial distribution...
Addressing potential local adaptation in species distribution models: implications for conservation under climate change
Maria Helena Hallfors, Jishan Liao, Jason D. K. Dzurisin, Ralph Grundel, Marko Hyvarinen, Kevin Towle, Grace C. Wu, Jessica J. Hellmann
2016, Ecological Applications (26) 1154-1169
Species distribution models (SDMs) have been criticized for involving assumptions that ignore or categorize many ecologically relevant factors such as dispersal ability and biotic interactions. Another potential source of model error is the assumption that species are ecologically uniform in their climatic tolerances across their range. Typically, SDMs to treat...
Female sea lamprey shift orientation toward a conspecific chemical cue to escape a sensory trap
Cory O. Brant, Nicholas S. Johnson, Ke Li, Tyler J. Buchinger, Weiming Li
2016, Behavioral Ecology (27) 810-819
The sensory trap model of signal evolution hypothesizes that signalers adapt to exploit a cue used by the receiver in another context. Although exploitation of receiver biases can result in conflict between the sexes, deceptive signaling systems that are mutually beneficial drive the evolution of stable communication systems. However, female...
Water-quality effects on phytoplankton species and density and trophic state indices at Big Base and Little Base Lakes, Little Rock Air Force Base, Arkansas, June through August, 2015
Lucas Driver, Billy Justus
2016, Journal of the Arkansas Academy of Science (70) 88-95
Big Base and Little Base Lakes are located on Little Rock Air Force Base, Arkansas, and their close proximity to a dense residential population and an active military/aircraft installation make the lakes vulnerable to water-quality degradation. The U.S. Geological Survey (USGS) conducted a study from June through August 2015 to investigate the effects of water quality on...
Evolution of mid-Atlantic coastal and back-barrier estuary environments in response to a hurricane: Implications for barrier-estuary connectivity
Jennifer L. Miselis, Brian D. Andrews, Robert S. Nicholson, Zafer Defne, Neil K. Ganju, Anthony S. Navoy
2016, Estuaries and Coasts (39) 916-934
Assessments of coupled barrier island-estuary storm response are rare. Hurricane Sandy made landfall during an investigation in Barnegat Bay-Little Egg Harbor estuary that included water quality monitoring, geomorphologic characterization, and numerical modeling; this provided an opportunity to characterize the storm response of the barrier island-estuary system. Barrier island morphologic response...
Quantifying watershed-scale groundwater loading and in-stream fate of nitrate using high-frequency water quality data
Matthew P. Miller, Anthony J. Tesoriero, Paul D. Capel, Brian A. Pellerin, Kenneth E. Hyer, Douglas A. Burns
2016, Water Resources Research (52) 330-347
We describe a new approach that couples hydrograph separation with high-frequency nitrate data to quantify time-variable groundwater and runoff loading of nitrate to streams, and the net in-stream fate of nitrate at the watershed-scale. The approach was applied at three sites spanning gradients in watershed size and land use in...
The East African monsoon system: Seasonal climatologies and recent variations: Chapter 10
Christopher C. Funk, Andrew Hoell, Shraddhanand Shukla, Gregory J. Husak, J. Michaelsen
2016, Book chapter, The Monsoons and Climate Change
This chapter briefly reviews the complex climatological cycle of the East African monsoon system, paying special attention to its connection to the larger Indo-Pacific-Asian monsoon cycle. We examine the seasonal monsoon cycle, and briefly explore recent circulation changes. The spatial footprint of our analysis corresponds with the “Greater Horn of...
Metabolic and physiochemical responses to a whole-lake experimental increase in dissolved organic carbon in a north-temperate lake
Jacob A. Zwart, Nicola Craig, Patrick T. Kelly, Stephen D. Sebestyen, Christopher T. Solomon, Brian Weidel, Stuart E. Jones
2016, Limnology and Oceanography (61) 723-734
Over the last several decades, many lakes globally have increased in dissolved organic carbon (DOC), calling into question how lake functions may respond to increasing DOC. Unfortunately, our basis for making predictions is limited to spatial surveys, modeling, and laboratory experiments, which may not accurately capture important whole-ecosystem processes. In...
Multi-scale predictions of massive conifer mortality due to chronic temperature rise
Nathan G. McDowell, A.P. Williams, C. Xu, W. T. Pockman, L. T. Dickman, Sanna Sevanto, R. Pangle, J. Limousin, J.J. Plaut, D.S. Mackay, J. Ogee, Jean-Christophe Domec, Craig D. Allen, Rosie A. Fisher, X. Jiang, J.D. Muss, D.D. Breshears, Sara A. Rauscher, C. Koven
2016, Nature Climate Change (6) 295-300
Global temperature rise and extremes accompanying drought threaten forests and their associated climatic feedbacks. Our ability to accurately simulate drought-induced forest impacts remains highly uncertain in part owing to our failure to integrate physiological measurements, regional-scale models, and dynamic global vegetation models (DGVMs). Here we show consistent predictions of widespread mortality of...
Soil amplification with a strong impedance contrast: Boston, Massachusetts
Laurie G. Baise, James Kaklamanos, Bradford M Berry, Eric M. Thompson
2016, Engineering Geology (202)
In this study, we evaluate the effect of strong sediment/bedrock impedance contrasts on soil amplification in Boston, Massachusetts, for typical sites along the Charles and Mystic Rivers. These sites can be characterized by artificial fill overlying marine sediments overlying glacial till and bedrock, where the depth to bedrock ranges from...
Spatial capture-recapture models allowing Markovian transience or dispersal
J. Andrew Royle, Angela K. Fuller, Chris Sutherland
2016, Population Ecology (58) 53-62
Spatial capture–recapture (SCR) models are a relatively recent development in quantitative ecology, and they are becoming widely used to model density in studies of animal populations using camera traps, DNA sampling and other methods which produce spatially explicit individual encounter information. One of the core assumptions of SCR models is...
Structure and spatial patterns of macrobenthic community in Tai Lake, a large shallow lake, China
Di Li, Richard A. Erickson, Song Tang, Xuwen Li, Zhichun Niu, Xia Wang, Hongling Liu, Hongxia Yu
2016, Ecological Indicators (61) 170-187
Tai Lake (Chinese: Taihu), the third-largest freshwater lake in China, suffers from harmful cyanobacteria blooms that are caused by economic development and population growth near the lake. Several studies have focused on phytoplankton in Tai Lake after a drinking water crisis in 2007; however, these studies primarily focused on microcystin bioaccumulation...
Climate change and water resources in a tropical island system: Propagation of uncertainty from statistically downscaled climate models to hydrologic models
Ashley E. Van Beusekom, William A. Gould, Adam J. Terando, Jaime A. Collazo
2016, International Journal of Climatology (36) 3370-3383
Many tropical islands have limited water resources with historically increasing demand, all potentially affected by a changing climate. The effects of climate change on island hydrology are difficult to model due to steep local precipitation gradients and sparse data. This work uses 10 statistically downscaled general circulation models (GCMs) under...
The effects of habitat, climate, and Barred Owls on long-term demography of Northern Spotted Owls
Katie M. Dugger, Eric D. Forsman, Alan B. Franklin, Raymond J. Davis, Gary C. White, Carl J. Schwarz, Kenneth P. Burnham, James D. Nichols, James E. Hines, Charles B. Yackulic, Paul F. Doherty, Larissa Bailey, Darren A. Clark, Steven H. Ackers, Lawrence S. Andrews, Benjamin Augustine, Brian L. Biswell, Jennifer Blakesley, Peter C. Carlson, Matthew J. Clement, Lowell V. Diller, Elizabeth M. Glenn, Adam Green, Scott A. Gremel, Dale R. Herter, J. Mark Higley, Jeremy Hobson, Rob B. Horn, Kathryn P. Huyvaert, Christopher McCafferty, Trent McDonald, Kevin McDonnell, Gail S. Olson, Janice A. Reid, Jeremy Rockweit, Viviana Ruiz, Jessica Saenz, Stan G. Sovern
2016, Condor (118) 57-116
Estimates of species' vital rates and an understanding of the factors affecting those parameters over time and space can provide crucial information for management and conservation. We used mark–recapture, reproductive output, and territory occupancy data collected during 1985–2013 to evaluate population processes of Northern Spotted Owls (Strix occidentalis caurina) in 11...
Soil moisture response to experimentally altered snowmelt timing is mediated by soil, vegetation, and regional climate patterns
Lafe G Conner, Richard A. Gill, Jayne Belnap
2016, Ecohydrology (9) 1006-1016
Soil moisture in seasonally snow-covered environments fluctuates seasonally between wet and dry states. Climate warming is advancing the onset of spring snowmelt and may lengthen the summer-dry state and ultimately cause drier soil conditions. The magnitude of either response may vary across elevation and vegetation types. We situated our study...
Radiometric dating of marine-influenced coal using Re–Os geochronology
Gyana Ranjan Tripathy, Judith L. Hannah, Holly J. Stein, Nicholas J. Geboy, Leslie F. Ruppert
2016, Earth and Planetary Science Letters (432) 13-23
Coal deposits are integral to understanding the structural evolution and thermal history of sedimentary basins and correlating contemporeous estuarine and fluvial delatic strata with marine sections. While marine shales may readily lend themselves to Re–Os dating due to the dominance of hydrogenous Re and Os,...
High and dry: high elevations disproportionately exposed to regional climate change in Mediterranean-climate landscapes
Ian M. McCullough, Frank W. Davis, John R. Dingman, Lorraine E. Flint, Alan L. Flint, Josep M. Serra-Diaz, Alexandra D. Syphard, Max A. Moritz, Lee Hannah, Janet Franklin
2016, Landscape Ecology (31) 1063-1075
Context Predicting climate-driven species’ range shifts depends substantially on species’ exposure to climate change. Mountain landscapes contain a wide range of topoclimates and soil characteristics that are thought to mediate range shifts and buffer species’ exposure. Quantifying fine-scale patterns of exposure across mountainous terrain is a...
Comparative demographics of a Hawaiian forest bird community
Alban Guillaumet, Bethany L. Woodworth, Richard J. Camp, Eben H. Paxton
2016, Journal of Avian Biology (47) 185-196
Estimates of demographic parameters such as survival and reproductive success are critical for guiding management efforts focused on species of conservation concern. Unfortunately, reliable demographic parameters are difficult to obtain for any species, but especially for rare or endangered species. Here we derived estimates of adult survival and recruitment in...
Non-linear resonant coupling of tsunami edge waves using stochastic earthquake source models
Eric L. Geist
2016, Geophysical Journal International (204) 878-891
Non-linear resonant coupling of edge waves can occur with tsunamis generated by large-magnitude subduction zone earthquakes. Earthquake rupture zones that straddle beneath the coastline of continental margins are particularly efficient at generating tsunami edge waves. Using a stochastic model for earthquake slip, it is shown that a wide range of...
Changes in seasonal climate outpace compensatory density-dependence in eastern brook trout
Ronald D. Bassar, Benjamin H. Letcher, Keith H. Nislow, Andrew R. Whiteley
2016, Global Change Biology (22) 577-593
Understanding how multiple extrinsic (density-independent) factors and intrinsic (density-dependent) mechanisms influence population dynamics has become increasingly urgent in the face of rapidly changing climates. It is particularly unclear how multiple extrinsic factors with contrasting effects among seasons are related to declines in population numbers and changes in mean body size...
Sustainable groundwater management in California
Steven P. Phillips, Laurel Lynn Rogers, Claudia C. Faunt
2016, Fact Sheet 2015-3084
The U.S. Geological Survey (USGS) uses data collection, modeling tools, and scientific analysis to help water managers plan for, and assess, hydrologic issues that can cause “undesirable results” associated with groundwater use. This information helps managers understand trends and investigate and predict effects of different groundwater-management strategies....
Conservation genomics reveals multiple evolutionary units within Bell’s Vireo (Vireo bellii).
Luke B. Klicka, Barbara E. Kus, Pascal O. Title, Kevin J. Burns
2016, Conservation Genetics (17) 455-471
The Bell’s Vireo (Vireo bellii) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current...
