Geology 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 …

Spatially Explicit Models For Inference About Density In Unmarked Or Partially Marked Populations, Richard B. Chandler, J. Andrew Royle

United States Geological Survey: Staff Publications

Recently developed spatial capture-recapture (SCR) models represent a major advance over traditional capture-recapture (CR) models because they yield explicit estimates of animal density instead of population size within an unknown area. Futhermore, unlike nonspatial CR methods, SCR models account for heterogeneity in capture probability arising from the juxtaposition of animal activity centers and sample locations. Although the utility of SCR methods is gaining recognition, the requirement that all individuals can be uniquely identified exludes their use in many contexts. In this paper, we develop models for situations in which individual recognition is not possible, thereby allowing SCR concepts to be …

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. …

Shelf-Scale Mapping Of Fish Distribution Using Active And Passive Acoustics, Carrie Christy Wall

USF Tampa Graduate Theses and Dissertations

Fish sound production has been associated with courtship and spawning behavior. Acoustic recordings of fish sounds can be used to identify distribution and behavior. Passive acoustic monitoring (PAM) can record large amounts of acoustic data in a specific area for days to years. These data can be collected in remote locations under potentially unsafe seas throughout a 24-hour period providing datasets unattainable using observer-based methods. However, the instruments must withstand the caustic ocean environment and be retrieved to obtain the recorded data. This can prove difficult due to the risk of PAMs being lost, stolen or damaged, especially in highly …

Deglacial Variability Of Antarctic Intermediate Water Penetration Into The North Atlantic From Authigenic Neodymium Isotope Ratios, Ruifang C. Xie, Franco Marcantonio, Matthew W. Schmidt

OES Faculty Publications

Understanding intermediate water circulation across the last deglacial is critical in assessing the role of oceanic heat transport associated with Atlantic Meridional Overturning Circulation variability across abrupt climate events. However, the links between intermediate water circulation and abrupt climate events such as the Younger Dryas (YD) and Heinrich Event 1 (H1) are still poorly constrained. Here, we reconstruct changes in Antarctic Intermediate Water (AAIW) circulation in the subtropical North Atlantic over the past 25 kyr by measuring authigenic neodymium isotope ratios in sediments from two sites in the Florida Straits. Our authigenic Nd isotope records suggest that there was little …

Solar Forcing Of Florida Straits Surface Salinity During The Early Holocene, Matthew W. Schmidt, William A. Weinlein, Franco Marcantonio, Jean Lynch-Stieglitz

OES Faculty Publications

Previous studies showed that sea surface salinity (SSS) in the Florida Straits as well as Florida Current transport covaried with changes in North Atlantic climate over the past two millennia. However, little is known about earlier Holocene hydrographic variability in the Florida Straits. Here, we combine Mg/Ca-paleothermometry and stable oxygen isotope measurements on the planktonic foraminifera Globigerinoides ruber (white variety) from Florida Straits sediment core KNR166-2 JPC 51 (24° 24.70' N, 83° 13.14' W, 198 m deep) to reconstruct a high-resolution (~25 yr/sample) early to mid Holocene record of sea surface temperature and δ¹⁸O_SW)(a …

A New Phase Speciation Leaching Procedure For The Determination Of Metals In Oxic And Anoxic Sediments, Brandon R. Gipson

OES Theses and Dissertations

Toxic trace elements such as cadmium, lead, chromium, and arsenic released by human activities can accumulate in marine and estuarine sediments, where these metals are often sequestered until local environmental changes (e.g., redox, salinity, and/or pH) allow these elements to be reintroduced into the food web. In order to assess the extent of toxic trace element contamination in sediment, numerous leaching schemes have been developed that separate sediment-bound trace metals into operationally defined geochemical phases. These "phase speciation" leaching schemes are typically designed with the purpose of being used on either oxic or anoxic sediments. However, natural sediments often contain …

Impact Of Abrupt Deglacial Climate Change On Tropical Atlantic Subsurface Temperatures, Matthew W. Schmidt, Ping Chang, Jennifer E. Hertzberg, Theodore R. Them Ii, Link Li, Bette L. Otto-Bliesner

OES Faculty Publications

Both instrumental data analyses and coupled ocean-atmosphere models indicate that Atlantic meridional overturning circulation (AMOC) variability is tightly linked to abrupt tropical North Atlantic (TNA) climate change through both atmospheric and oceanic processes. Although a slowdown of AMOC results in an atmospheric-induced surface cooling in the entire TNA, the subsurface experiences an even larger warming because of rapid reorganizations of ocean circulation patterns at intermediate water depths. Here, we reconstruct high-resolution temperature records using oxygen isotope values and Mg/Ca ratios in both surface- and sub-thermocline-dwelling planktonic foraminifera from a sediment core located in the TNA over the last 22 ky. …

Topographic Control Of Asynchronous Glacial Advances: A Case Study From Annapurna, Nepal, Beth Pratt-Sitaula, Douglas W. Burbank, Arjun M. Heimsath, Neil F. Humphrey, Michael Oskin, Jaakko Putkonen

All Faculty Scholarship for the College of the Sciences

Differences in the timing of glacial advances, which are commonly attributed to climatic changes, can be due to variations in valley topography. Cosmogenic 10Be dates from 24 glacial moraine boulders in 5 valleys define two age populations, late-glacial and early Holocene. Moraine ages correlate with paleoglacier valley hypsometries. Moraines in valleys with lower maximum altitudes date to the lateglacial, whereas those in valleys with higher maximum altitudes are early Holocene. Two valleys with similar equilibrium-line altitudes (ELAs), but contrasting ages, are < 5 km apart and share the same aspect, such that spatial differences in climate can be excluded. A glacial mass-balance cellular automata model of these two neighboring valleys predicts that change from a cooler-drier to warmer-wetter climate (as at the Holocene onset) would lead to the glacier in the higher altitude catchment advancing, while the lower one retreats or disappears, even though the ELA only shifted by ~120 m.

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 …

Identifying Changes In Climatic Trends And The Fingerprints Of Landuse And Landcover Changes In The High Plains Of The Usa, Denis Mutiibwa

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

Human activities such as conversion of natural ecosystem to croplands and urban-centers, deforestation and afforestation impact biophysical properties of land surface such as albedo, energy balance, and surface roughness. Alterations in these properties affect the heat and moisture exchanges between the land surface and atmospheric boundary layer. The objectives of this research were; (i) to quantitatively identify the High plains’ regional climate change in temperatures over the period 1895 to 2006, (ii) detect the signatures of anthropogenic forcing of LULC changes on the regional climate change of the High Plains, and (iii) examine the trends in evolving regional latent heat …

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 …

Pleistocene Climate In Alaska From Stable Isotopes In An Ice Wedge, Corinne Y. Griffing

UNLV Theses, Dissertations, Professional Papers, and Capstones

The CRREL permafrost tunnel offers a unique opportunity to sample ice wedges in a climate-controlled environment, penetrating frozen silts which host massive ground ice that may record Dansgaard-Oeschger (D-O) and Heinrich Events. Ice wedges in the tunnel have been dated to approximately 36-22 ka (Hamilton et al., 1988), allowing the paleoclimate of the region to be reconstructed during MIS 3, when D-O and Heinrich events were documented in various other records. These climate cycles are rapid climate oscillations that have been recognized in records from the Arctic and subarctic, and suggest that climate can rapidly shift by 10°C over millennial …

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 …

The Role Of Underflows And Climate On Sediment Distribution In Glacial-Fed Lake Linné, Svalbard, Norway, Diana Zamora-Reyes^, Vanessa L. Lougheed, Alan Werner, Steven Roof*

COURI Symposium Abstracts, Spring 2011

Linnévatnet (78° 2’N, 13° 49’E), is a glacial-fed lake located in Svalbard, an archipelago north of Norway. Sediments found in the lake are supplied by the Linné Glacier, 8km south of the lake, and are transported by the melt stream into the lake, creating laminations with a strong signal of seasonal deposition. Due to its immaculate environment and recent rapid increase in temperature, this site is an ideal place to study past-climate proxies and determine how the changing environment is affecting the area. The objective of this study is to determine the frequency of water underflows influencing sediment distribution and …

Recent Increase In Black Carbon Concentrations From A Mt. Everest Ice Core Spanning 1860-2000 Ad, Susan D. Kaspari, M. Schwikowski, M. Gysel, M. G. Flanner, S. Kang, S. Hou, P. A. Mayewski

All Faculty Scholarship for the College of the Sciences

A Mt. Everest ice core spanning 1860–2000 AD and analyzed at high resolution for black carbon (BC) using a Single Particle Soot Photometer (SP2) demonstrates strong seasonality, with peak concentrations during the winter‐spring, and low concentrations during the summer monsoon season. BC concentrations from 1975–2000 relative to 1860–1975 have increased approximately threefold, indicating that BC from anthropogenic sources is being transported to high elevation regions of the Himalaya. The timing of the increase in BC is consistent with BC emission inventory data from South Asia and the Middle East, however since 1990 the ice core BC record does not indicate …

Reproduction And Genetic Detection Of Veligers In Changing Dreissena Populations In The Great Lakes, Jeffrey L. Ram, Aos S. Karim, Payel Acharya, Pranav Jagtap, Sonal Purohit, Donna R. Kashian

Environmental Science and Geology Faculty Research Publications

Dreissenid bivalves, Dreissena polymorpha (zebra mussel) and Dreissena bugensis (quagga mussel) are biofouling species that invaded the Great Lakes region of North America from source populations in Europe in the 1980s. Initially, D. polymorpha spread faster and farther; however, D. bugensis have recently displaced D. polymorpha in many areas of the Great Lakes and was the first to be found west of the Continental Divide. Early detection of dreissenids is important in anticipating and preventing potentially high economic impacts. To study population dynamics and to enhance detection methods, we assessed “spawnability” using a serotonin bioassay and developed a new, sensitive, …

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 …

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 …