Oceanography and Atmospheric Sciences and Meteorology Commons^™

On Thinning Of Chains In Mcmc, William A. Link, Mitchell J. Eaton

United States Geological Survey: Staff Publications

1. Markov chain Monte Carlo (MCMC) is a simulation technique that has revolutionised the analysis of ecological data, allowing the fitting of complex models in a Bayesian framework. Since 2001, there have been nearly 200 papers using MCMC in publications of the Ecological Society of America and the British Ecological Society, including more than 75 in the journal Ecology and 35 in the Journal of Applied Ecology.

2. We have noted that many authors routinely ‘thin’ their simulations, discarding all but every kth sampled value; of the studies we surveyed with details on MCMC implementation, 40% reported thinning.

3. Thinning …

Sea-Level History During The Last Interglacial Complex On San Nicolas Island, California: Implications For Glacial Isostatic Adjustment Processes, Paleozoogeography And Tectonics, Daniel R. Muhs, Kathleen R. Simmons, R. Randall Schumann, Lindsey T. Groves, Jerry X. Mitrovica, Deanna Laurel

United States Geological Survey: Staff Publications

San Nicolas Island, California has one of the best records of fossiliferous Quaternary marine terraces in North America, with at least fourteen terraces rising to an elevation of ~270 m above present-day sea level. In our studies of the lowest terraces, we identified platforms at 38–36 m (terrace 2a), 33–28 m (terrace 2b), and 13–8 m (terrace 1). Uranium-series dating of solitary corals from these terraces yields three clusters of ages: ~120 ka on terrace 2a (marine isotope stage [MIS] 5.5), ~120 and ~100 ka on terrace 2b (MIS 5.5 and 5.3), and ~80 ka (MIS 5.1) on terrace 1.We …

Tectonic Influences On The Preservation Of Marine Terraces: Old And New Evidence From Santa Catalina Island, California, R. Randall Schumann, Scott A. Minor, Daniel R. Muhs, Lindsey T. Groves, John P. Mcgeehan

United States Geological Survey: Staff Publications

The California Channel Islands contain some of the best geologic records of past climate and sea-level changes, recorded in uplifted, fossil-bearing marine terrace deposits. Among the eight California Channel Islands and the nearby Palos Verdes Hills, only Santa Catalina Island does not exhibit prominent emergent marine terraces, though the same terrace-forming processes that acted on the other Channel Islands must also have occurred on Santa Catalina. We re-evaluated previous researchers' field evidence and examined new topographic, bathymetric, and stream-profile data in order to find possible explanations for the lack of obvious marine terrace landforms or deposits on the island today. …

Spring Migration Of Mallards From Arkansas As Determined By Satellite Telemetry, David George Krementz, Kwasi Asante, Luke W. Naylor

United States Geological Survey: Staff Publications

We used satellite telemetry to document spring migration phenology, routes, stopover regions, and nesting sites of mallards Anas platyrhynchos marked in Arkansas during the winters of 2004–2007. Of the 143 marked mallards that migrated from Arkansas, they did so, on average, by mid-March. Mallards flew over the Missouri Ozarks and 42% made an initial stopover in Missouri, where they used areas that had larger rivers (Mississippi River, Missouri River) embedded in an agricultural landscape. From this stopover region they either migrated directly to the Prairie Pothole Region (PPR) or they migrated north to Minnesota where they either moved next to …

Droughtscape, Fall 2011, Kelly Smith

DroughtScape: Quarterly Newsletter of the National Drought Mitigation Center (2007–2023)

Drought Preparedness Community Options

Drought Likely to Persist, Intensify Across South

Database Will Help Planners Find Options

Impacts: Ag Losses, Fire, Water Restrictions

NDMC Welcomes International Visitors

New Drought Impact Reporter Online

Sim-Drought, Available Now at Select Agencies

Do Wind Turbines Affect Weather Conditions?: A Case Study In Indiana, Meghan F. Henschen, Brittany Herrholtz, Lacey Rhudy, Kathryn Demchak, Brian Doogs, Joshua Holland, Erik Larson, Johnny Martin, Matthew Rudkin

The Journal of Purdue Undergraduate Research

Wind turbines are becoming increasingly widespread in the United States as the world looks for cleaner sources of energy. Scientists, policymakers, and citizens have strong opinions regarding the positive and negative effects of wind energy projects, and there is a great deal of misinformation about wind energy circulating on the Web and other media sources. The purpose of this study is to gain a better understanding of how the rotation of hundreds of turbines can influence local weather conditions within a wind farm and in the surrounding areas. This experiment measures temperature, atmospheric pressure, wind speed, wind direction, relative humidity, …

Droughtscape, Summer 2011, Kelly Smith

DroughtScape: Quarterly Newsletter of the National Drought Mitigation Center (2007–2023)

New NDMC Website

Drought May Improve in Southeast and Southwest

Impacts Summary: Fire, Crop Loss and More

International Activities

NDMC Launches Ranch Planning Tool

Serving Data to Order

Workshop Builds Drought Planning Community

Secretive Marsh Bird Species Co-Occurrences And Habitat Associations Across The Midwest, Usa, Jason R. Bolenbaugh, Sarah E. Lehnen, David G. Krementz

United States Geological Survey: Staff Publications

Because secretive marsh birds are difficult to detect, population status and habitat use for these birds are not well known. We conducted repeated surveys for secretive marsh birds across 264 sites in the Upper Mississippi River and Great Lakes Joint Venture region to estimate abundance, occupancy, and detection probabilities during the 2008 and 2009 breeding seasons. We identified species groups based on observed species co-occurrences. Two species, least bittern Ixobrychus exilis and American bittern Botaurus lentiginosus, co-occurred with other species less often than expected by chance, and two species groups, rails (Virginia rail Rallus limicola and sora Porzana carolina) and …

Rapid Wetland Expansion During European Settlement And Its Implication For Marsh Survival Under Modern Sediment Delivery Rates, Matthew L. Kirwan, A. Brad Murray, Jeffrey P. Donnelly, D. Reide Corbett

United States Geological Survey: Staff Publications

Fluctuations in sea-level rise rates are thought to dominate the formation and evolution of coastal wetlands. Here we demonstrate a contrasting scenario in which land-use–related changes in sediment delivery rates drive the formation of expansive marshland, and vegetation feedbacks maintain their morphology despite recent sediment supply reduction. Stratigraphic analysis and radiocarbon dating in the Plum Island Estuary (Massachusetts, United States) suggest that salt marshes expanded rapidly during the eighteenth and nineteenth centuries due to increased rates of sediment delivery following deforestation associated with European settlement. Numerical modeling coupled with the stratigraphic observations suggests that existing marshland could survive, but not …

Spatial Patterns Of Drought Triggers And Indicators, Joseph P. Robine

Department of Environmental Studies: Undergraduate Student Theses

Drought is a reoccurring phenomenon with widespread economic, social, and environmental impacts. Unlike other disasters, a drought cannot be easily detected. In addition, droughts are widespread and develop slowly over time making it difficult to detect its onset and monitor its severity and impacts. To assist in monitoring the severity and spatial extent of droughts, drought managers frequently use indicators and triggers. Drought indicators are meteorological or hydrological variables or indices that quantify or describe the level of drought severity. A drought trigger is a value of an indicator that initiates management and response actions. Despite the clear importance of …

Extent Of Gully Erosion In An Agricultural Field In Northeastern Nebraska At Section 35 Township 29 North Range 1 West In Cedar County, Crystal Starkel

Department of Environmental Studies: Undergraduate Student Theses

My thesis project examined a gully within Section 35 Township 29 North Range 1 West. This gully has been noticed for five years and has grown substantially in those five years. The extent and causes of gully erosion were examined by considering the soil, the climate, the land management history, by measuring the gully physically, by using GIS, and by using an economic support tool was estimate soil loss. Appropriate recommendations were developed to reduce gully erosion.

Effects Of Rodent Species, Seed Species, And Predator Cues On Seed Fate, Kelly J. Sivy, Steven M. Ostoja, Eugene W. Schupp, Susan Durham

United States Geological Survey: Staff Publications

Seed selection, removal and subsequent management by granivorous animals is thought to be a complex interaction of factors including qualities of the seeds themselves (e.g., seed size, nutritional quality) and features of the local habitat (e.g. perceived predator risk). At the same time, differential seed selection and dispersal is thought to have profound effects on seed fate and potentially vegetation dynamics. In a feeding arena, we tested whether rodent species, seed species, and indirect and direct predation cues influence seed selection and handling behaviors (e.g., scatter hoarding versus larder hoarding) of two heteromyid rodents, Ord’s kangaroo rat (Dipodomys ordii) and …

Droughtscape, Spring 2011, Kelly Smith

DroughtScape: Quarterly Newsletter of the National Drought Mitigation Center (2007–2023)

Register Now

Forecasters Say Dryness in TX and SW to Continue

Drought Planning, The Game: Coming Soon

Ding Takes New Post

South and Southwest Lose Crops, Fight Fires

Drought Monitor Authors Review Enhanced GIS Tools and New Processes

Evaluation Of The Sensitivity Of Inventory And Monitoring National Parks To Acidification Effects From Atmospheric Sulfur And Nitrogen Deposition, Northern Great Plains Network (Ngpn), T. J. Sullivan, T. C. Mcdonnell, G. T. Mcpherson, S. D. Mackey, D. Moore

United States National Park Service: Publications

Northern Great Plains Network (NGPN)

National maps of atmospheric sulfur (S) and nitrogen (N) emissions and deposition are provided in Maps A through D as context for subsequent network data presentations. Maps A and B show county level emissions of total S and total N for the year 2002. Maps C and D show total S and total N deposition, again for the year 2002.

There are three parks in the Northern Great Plains Network that are larger than 100 square miles: Badlands (BADL), Missouri (MNRR), and Theodore Roosevelt (THRO). In addition, there are 10 smaller parks.

Total annual S …

Evaluation Of The Sensitivity Of Inventory And Monitoring National Parks To Nutrient Enrichment Effects From Atmospheric Nitrogen Deposition Northern Great Plains Network (Ngpn), T. J. Sullivan, T. C. Mcdonnell, G. T. Mcpherson, S. D. Mackey, D. Moore

United States National Park Service: Publications

Northern Great Plains Network (NGPN)

National maps of atmospheric N emissions and deposition are provided in Maps A and B as context for subsequent network data presentations. Map A shows county level emissions of total N for the year 2002. Map B shows total N deposition, again for the year 2002.

There are three parks in the Northern Great Plains Network that are larger than 100 square miles: Badlands (BADL), Missouri (MNRR), and Theodore Roosevelt (THRO). In addition, there are 10 other smaller parks.

Total annual N emissions, by county, are shown in Map C for lands in and surrounding …

Estimating Age From Recapture Data: Integrating Incremental Growth Measures With Ancillary Data To Infer Age-At-Length, Mitchell J. Eaton, William A. Link

United States Geological Survey: Staff Publications

Estimating the age of individuals in wild populations can be of fundamental importance for answering ecological questions, modeling population demographics, and managing exploited or threatened species. Significant effort has been devoted to determining age through the use of growth annuli, secondary physical characteristics related to age, and growth models. Many species, however, either do not exhibit physical characteristics useful for independent age validation or are too rare to justify sacrificing a large number of individuals to establish the relationship between size and age. Length-at-age models are well represented in the fisheries and other wildlife management literature. Many of these models …

The Role Of Demographic Compensation Theory In Incidental Take Assessments For Endangered Species, Conor P. Mcgowan, Mark R. Ryan, Michael C. Runge, Joshua J. Millspaugh, Jean Fitts Cochrane

United States Geological Survey: Staff Publications

Many endangered species laws provide exceptions to legislated prohibitions through incidental take provisions as long as take is the result of unintended consequences of an otherwise legal activity. These allowances presumably invoke the theory of demographic compensation, commonly applied to harvested species, by allowing limited harm as long as the probability of the species’ survival or recovery is not reduced appreciably. Demographic compensation requires some density-dependent limits on survival or reproduction in a species’ annual cycle that can be alleviated through incidental take. Using a population model for piping plovers in the Great Plains, we found that when the population …

Selenium In Birds, Harry M. Ohlendorf, Gary H. Heinz

United States Geological Survey: Staff Publications

Selenium (Se) is a metalloid trace element that birds and other wildlife need in small amounts for good health. The main purpose of this chapter is to interpret tissue concentrations of Se. However, because food is the main source of Se accumulation for birds and other wildlife, and because dietary concentrations for effects on bird reproduction have been reported, we also provide interpretive information on Se in the diet.

Se deficiencies in domestic poultry and livestock occur in some parts of the world and must be corrected by additions of Se to the diet. However, the range of dietary concentrations …

History Of Wildlife Toxicology And The Interpretation Of Contaminant Concentrations In Tissues, Barnett A. Rattner, Anton M. Scheuhammer, John E. Ellott

United States Geological Survey: Staff Publications

The detection and interpretation of contaminants in tissues of wildlife belongs to the field of toxicology, a scientific discipline with a long, intriguing, and illustrious history (reviewed by Hayes 1991, Gallo 2001, Gilbert and Hayes 2006, Wax 2006). We review its history briefly, to provide a context for understanding the use of tissue residues in toxicology, and to explain how their use has developed over time. Because so much work has been conducted on mercury, and dioxins and polychlorinated biphenyls (PCBs), separate case histories are included that describe the evolution of the use of tissue concentrations to assess exposure and …

Droughtscape, Winter 2011, Kelly Smith

DroughtScape: Quarterly Newsletter of the National Drought Mitigation Center (2007–2023)

Register for the U.S. Drought Monitor Forum

La Niña Brings Southeast, Southwest Drought

International Efforts

Drought Returns in 2010

Impacts Emerge “Before” Summer Drought in East

October-December Quarterly Impacts Summary

Climate Adaptation for Local Government

NDMC Elicits Missouri River Basin Recollections

Woudenberg Coordinates Educational Booklet

The Rise And Fall Of Lake Bonneville Between 45 And 10.5 Ka, L.V. Benson, S.P. Lund, J.P. Smoot, D.E. Rhode, R.J. Spencer, K.L. Verosub, L.A. Louderback, C.A. Johnson, R.O. Rye, R.M. Negrini

United States Geological Survey: Staff Publications

A sediment core taken from the western edge of the Bonneville Basin has provided high-resolution proxy records of relative lake-size change for the period 45.1-10.5 calendar ka (hereafter ka). Age control was provided by a paleomagnetic secular variation (PSV)-based age model for Blue Lake core BL04-4. Continuous records of δ¹⁸O and total inorganic carbon (TIC) generally match an earlier lake-level envelope based on outcrops and geomorphic features, but with differences in the timing of some hydrologic events/states. The Stansbury Oscillation was found to consist of two oscillations centered on 25 and 24 ka. Lake Bonneville appears to have …

Adaptive Resource Management And The Value Of Information, Byron K. Williams, Mitchell J. Eaton, David R. Breininger

United States Geological Survey: Staff Publications

The value of information is a general and broadly applicable concept that has been used for several decades to aid in making decisions in the face of uncertainty. Yet there are relatively few examples of its use in ecology and natural resources management, and almost none that are framed in terms of the future impacts of management decisions. In this paper we discuss the value of information in a context of adaptive management, in which actions are taken sequentially over a time frame and both future resource conditions and residual uncertainties about resource responses are taken into account. Our objective …

Evaluating Spawning Migration Patterns And Predicting Spawning Success Of Shovelnose Sturgeon In The Lower Missouri River, M. L. Wildhaber, S. H. Holan, G. M. Davis, D. W. Gladish, A. J. Delonay, Diana M. Papoulias, D. K. Sommerhauser

United States Geological Survey: Staff Publications

Approaches using telemetry, precise reproductive assessments, and surgically implanted data storage tags (DSTs) were used in combination with novel applications of analytical techniques for fish movement studies to describe patterns in migratory behavior and predict spawning success of gravid shovelnose sturgeon. From 2004 to 2007, over 300 gravid female shovelnose sturgeon (Scaphirhynchus platorynchus) from the Lower Missouri River, that were expected to spawn in the year they were collected, were surgically implanted with transmitters and archival DSTs. Functional cluster modeling of telemetry data from the spawning season suggested two common migration patterns of gravid female shovelnose sturgeon. Fish …

Land Change Variability And Human–Environment Dynamics In The United States Great Plains, Mark A, Drummond, Roger F. Auch, Krista A. Karstensen, Kristi L. Sayler, Janis L. Taylor, Thomas Loveland

United States Geological Survey: Staff Publications

Land use and land cover changes have complex linkages to climate variability and change, biophysical resources, and socioeconomic driving forces. To assess these land change dynamics and their causes in the Great Plains, we compare and contrast contemporary changes across 16 ecoregions using Landsat satellite data and statistical analysis. Large-area change analysis of agricultural regions is often hampered by change detection error and the tendency for land conversions to occur at the local-scale. To facilitate a regional-scale analysis, a statistical sampling design of randomly selected 10 km × 10 km blocks is used to efficiently identify the types and rates …

Introduction To “Environmental Contaminants In Biota, 2nd Edition”, W. Nelson Beyer, James P. Meador

United States Geological Survey: Staff Publications

Ecotoxicology is the study of the movement of environmental contaminants through ecosystems and their effects on plants and animals. Examining tissue residues of these contaminants in biota is basic to ecotoxicology, both for understanding the movement of contaminants within organisms and through food chains, and for understanding and quantifying injuries to organisms and their communities. This book provides guidance on interpreting tissue concentrations of environmental contaminants.

Tissue concentrations have long been used both to identify the cause of toxicity in animals and as a measure of the severity of toxicity. More recently, they have been incorporated into environmental models, tying …

Lead In Birds, J. Christian Franson, Deborah J. Pain

United States Geological Survey: Staff Publications

Lead is a highly toxic heavy metal that acts as a nonspecific poison affecting all body systems and has no known biological requirement. Absorption of low concentrations may result in a wide range of sublethal effects in animals, and higher concentrations may result in mortality (Demayo et al. 1982).

Lead has been mined and smelted by humans for centuries, but the use of lead-based products increased greatly following the Industrial Revolution. Consequently, lead today is ubiquitous in air, water, and soil, in both urban and rural environments (Eisler 2000). Vertebrates are exposed to lead mainly via inhalation and ingestion. A …

Spatial Patch Occupancy Patterns Of The Lower Keys Marsh Rabbit, Mitchell J. Eaton, Phillip T. Hughes, James D. Nichols, Anne Morkill, Chad Anderson

United States Geological Survey: Staff Publications

Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naı¨ve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats.

Estimating Age From Recapture Data: Integrating Incremental Growth Measures With Ancillary Data To Infer Age-At-Length, Mitchell J. Eaton, William A. Link

United States Geological Survey: Staff Publications

Estimating the age of individuals in wild populations can be of fundamental importance for answering ecological questions, modeling population demographics, and managing exploited or threatened species. Significant effort has been devoted to determining age through the use of growth annuli, secondary physical characteristics related to age, and growth models. Many species, however, either do not exhibit physical characteristics useful for independent age validation or are too rare to justify sacrificing a large number of individuals to establish the relationship between size and age. Length-at-age models are well represented in the fisheries and other wildlife management literature. Many of these models …

Spatial Patch Occupancy Patterns Of The Lower Keys Marsh Rabbit, Mitchell J. Eaton, Phillip T. Hughes, James D. Nichols, Anne Morkill, Chad Anderson

United States Geological Survey: Staff Publications

Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naı¨ve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats.

Rapid Wetland Expansion During European Settlement And Its Implication For Marsh Survival Under Modern Sediment Delivery Rates, Matthew L. Kirwan, A. Brad Murray, Jeffrey P. Donnelly, D. Reide Corbett

United States Geological Survey: Staff Publications

Fluctuations in sea-level rise rates are thought to dominate the formation and evolution of coastal wetlands. Here we demonstrate a contrasting scenario in which land-use–related changes in sediment delivery rates drive the formation of expansive marshland, and vegetation feedbacks maintain their morphology despite recent sediment supply reduction. Stratigraphic analysis and radiocarbon dating in the Plum Island Estuary (Massachusetts, United States) suggest that salt marshes expanded rapidly during the eighteenth and nineteenth centuries due to increased rates of sediment delivery following deforestation associated with European settlement. Numerical modeling coupled with the stratigraphic observations suggests that existing marshland could survive, but not …