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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 …

Atr-Ftir Studies On The Kinetics Of Dimethylarsinic Acid (Dma) Surface Complexation With Iron(Oxyhydr)Oxides, Julia Tofan-Lazar Miss

Theses and Dissertations (Comprehensive)

Dimethylarsinic acid (DMA) is an organoarsenical compound that, along with monomethylarsonic acid, poses a health and an environmental risk, and a challenge to the energy industry. Little is known about the surface chemistry of DMA at the molecular level with materials relevant to geochemical environments and industrial sectors. The surface chemistry of phosphorus and arsenic compounds in their organic and inorganic forms is of great interest due to its role in controlling their transport, bioaccessibility and speciation. This thesis reports the first in-situ and surface-sensitive rapid kinetic studies on the adsorption and desorption of DMA to and from Fe-(oxyhydr)oxide films …

Climate Change At The Pleistocene-Holocene Boundary In The Pacific Northwest: A Comparison Of Proxy Datasets And The Archaeologicial Record, Tiffany J. Fulkerson

EWU Masters Thesis Collection

"The relationship between climate change at the Pleistocene-Holocene Boundary (ca. 12,600-10,200 cal B.P.) and cultural responses to attendant shifts in the environment remains a vexing issue for archaeologists. This study compiles and analyzes glacial, palynological, faunal, and stratigraphic/geomorphological proxy datasets for climate change in the Pacific Northwest of North America and compares them to the coeval archaeological record. The primary purpose of this exercise is to consider the potential ways in which climate change at the Pleistocene-Holocene Boundary affected cultural development for Late Paleoindian-Early Archaic peoples in the Pacific Northwest. Results indicate that climatic and environmental change at this interval …

Stable Isotope Analysis Of Busycon Sinistrum To Determine Fort Walton-Period Seasonality At St. Joseph Bay, Northwest Florida, Ryan Michael Harke

USF Tampa Graduate Theses and Dissertations

ABSTRACT

Recent archaeological investigations indicate that coastal Fort Walton cultures in the St. Joseph Bay region of northwest Florida emphasized marine and estuarine foraging. These late prehistoric (A.D. 1000-1500) peoples collected fish, shellfish, and other aquatic resources. At the Richardson's Hammock site (8Gu10), radiocarbon-dated to about A.D. 1300, as at dozens of other shell middens around this salty bay, large gastropods were a major subsistence component. This adaptation is in sharp contrast with that of contemporaneous inland Fort Walton societies, who relied on maize agriculture. It is unknown whether coastal groups represent separate hunter-gatherer-fisher populations or seasonal migrations by inland …

Comparative Microbial Sampling From Eutrophic Caves In Slovenia And Slovakia Using Rida ®Count Test Kits, Janez Mulec, Václav Krištůfek, Alica Chroňáková

International Journal of Speleology

RIDA®COUNT test plates were used as an easy-to-handle and rapid indicator of microbial counts in karst ecosystems of several caves in Slovakia and Slovenia. All of the caves had a high organic input from water streams, tourists, roosting bat colonies or terrestrial surroundings. We sampled swabs, water and air samples to test robustness and universality of the RIDA®COUNT test kit (R-Biopharm AG, Germany, http://www.r-biopharm.com/) for quantification of total bacteria, coliforms, yeast and mold. Using data from swabs (colony-forming units per cm²) we proposed a scale for description of biocontamination level or superficial microbial load of cave niches. Based …

Relationship Between Carbon Dioxide In Balcarka Cave And Adjacent Soils In The Moravian Karst Region Of The Czech Republic, Jiří Faimon, Monika Ličbinská, Petr Zajíček

International Journal of Speleology

Carbon dioxide concentration, air temperature, and humidity were monitored at (1) two cave sites and (2) three adjacent karst soils. The data over a one-year period are supported by dripwater chemistry and cave visiting frequency. The results indicate that the sources of cave CO2 are anthropogenic and epikarstic ones in addition to ordinary soils. Epikarstic CO2 produced under almost stationary conditions probably control dripwater chemistry and cave’s CO2 maxima. Based on breathing and door opening, anthropogenic activity affects instantaneous cave CO2 levels, depending on site volume/position and visitor number. A conceptual model of the CO2 dynamics of the soil-cave system …

Diversity And Community Assembly Patterns Of Epigean Vs. Troglobiont Spiders In The Iberian Peninsula, Pedro Cardoso

International Journal of Speleology

Cave-obligate organisms usually have smaller ranges and their assemblages have higher beta diversity than their epigean counterparts. Phylogenetic and functional diversity is usually low in cave communities, leading to taxonomic and functional disharmony, with entire groups missing from the subterranean realm. The objective of this work is to compare range, beta diversity, phylogenetic and functional diversity, taxonomic and functional disharmony of epigean versus troglobiont spiders in the Iberian Peninsula.

The median extent of occurrence was found to be 33 times higher for epigean than for cave species. Beta diversity was significantly higher for troglobiont assemblages. Cave assemblages present lower phylogenetic …

Chemical Defense In The Cave-Dwelling Millipede Brachydesmus Troglobius Daday, 1889 (Diplopoda, Polydesmidae), Slobodan E. Makarov, Ljubodrag V. Vujisić, Božidar P. M. Ćurčić, Bojan S. Ilić, Vele V. Tešević, Vlatka E. Vajs, Ivan M. Vučković, Bojan M. Mitić, Luka R. Lučić, Iris Ž. Đorđević

International Journal of Speleology

The troglomorphic millipede Brachydesmus troglobius Daday, 1889 (Polydesmida: Polydesmidae) secretes allomones from glands on both lateral surfaces of its body segments. The secretion was identified by gas chromatography-mass spectrometry (GC-MS) analysis with electron and chemical ionization, and was shown to be composed of a mixture of benzaldehyde, benzyl alcohol, benzoylnitrile, benzoic acid and mandelonitrile benzoate. Hydrogen cyanide was qualitatively identified by the picric acid test. This is the first identification of these compounds in a cave-dwelling polydesmid.

Volcanic Caves: Priorities For Conserving The Azorean Endemic Troglobiont Species, Paulo A.V. Borges Prof., Pedro Cardoso, Isabel R. Amorim, Fernando Pereira, João P. Constância, João C. Nunes, Paulo Barcelos, Paulino Costa, Rosalina Gabriel, Maria L. Dapkevicius

International Journal of Speleology

Azorean lava-tubes and volcanic pits adequately sampled for arthropod fauna were evaluated for species diversity and rarity. An iterative partial multiple regression analysis was performed to produce a multi-criteria index (Importance Value for Cave Conservation, IV-CC) incorporating arthropod species diversity indices but also including indices qualifying cave geological and management features (e.g., the diversity of geological structures, threats, accessibility). Additionally, we calculated complementarity solutions (irreplaceability and Fraction-of-Spare measures) for each cave with different targets per species, i.e., the minimum number of caves needed for each species to be represented either once or twice. Our results clearly show that to preserve …

Bacterial Community Survey Of Sediments At Naracoorte Caves, Australia, Eric M. Adetutu, Krystal Thorpe, Esmaeil Shahsavari, Steven Bourne, Xiangsheng Cao, Ramin Mazaheri Nezhad Fard, Greg Kirby, Andrew S. Ball

International Journal of Speleology

Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial diversity in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible) and control caves. Sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey …

The World’S Deepest Subterranean Community - Krubera-Voronja Cave (Western Caucasus), Alberto Sendra, Ana Sofia P.S. Reboleira

International Journal of Speleology

Subsurface biota extends over a wide variety of habitats that can be spatially interconnected. The largest communities of this subsurface biota inhabit cavities and are well known mainly in caves where biologists are able to have access. Data about deep subterranean communities and arthropods living under one thousand meters was unknown.

An expedition to world’s deepest cave, Krubera-Voronja in Western Caucasus, revealed an interesting subterranean community, living below 2000 meters and represented by more than 12 species of arthropods, including several new species for science. This deep cave biota is composed of troglobionts and also epigean species, that can penetrate …

A Large Cervidae Holocene Accumulation In Eastern Brazil: An Example Of Extreme Taphonomical Control In A Cave Environment, Alex Hubbe, Augusto S. Auler

International Journal of Speleology

A remarkable cervid bone accumulation occurs at a single passage (named Cervid Passage; CP) at Lapa Nova, a maze cave in eastern Brazil. CP lies away from cave entrances, is a typical pitfall passage and contains bone remains of at least 121 cervids, besides few bats, peccaries and rodents remains. There is no evidence of water (or sediment) flow at the site and in general bones lack post depositional alterations and display anatomical proximity, suggesting that the majority of the remains found inside CP (mainly cervids) are due to animals that after entering the cave got trapped in the site. …

Management In A Neotropical Show Cave: Planning For Invertebrates Conservation, Thais Giovannini Pellegrini, Rodrigo Lopes Ferreira

International Journal of Speleology

Lapa Nova is a dolomitic cave about 4.5 km long located in northwestern Minas Gerais state, Brazil. The cave experiences intense tourism, concentrated over a single period of the year, during the Feast of Our Lady of Lapa. In order to evaluate the impacts felt by the invertebrate community from this tourism, a new methodology was proposed. Four types of areas (intense visitation area, outlying visitation areas, moderate visitation areas and no-visitation areas) were sampled for invertebrates. There was one sampling prior and another on the last day of the 128^th feast, to evaluate the effects of visitation on …

San Miguel Volcanic Seismicity And Structure In Central America: Insight Into The Physical Processes Of Volcanoes, Ezer Patlan

Open Access Theses & Dissertations

San Miguel volcano lies near the city of San Miguel, El Salvador (13.43°N, 88.26°W). An active stratovolcano, it presents a significant natural hazard for the city of San Miguel. In general, the internal state and activity of volcanoes like San Miguel remains an important component to understanding volcanic hazards. The main technology for addressing volcanic hazards and associated processes is through the analysis of data collected from the deployment of seismic sensors that record ground motion. Six seismic stations were deployed by UTEP around San Miguel volcano during the 2007-2008 the time period to define internal structure or magmatic plumbing …

Would Predatory Drillhole Frequency On Chione Spp. Increase Under The Suggested Climate Change Scenario? Comparing Pleistocene And Modern Rhodolith Beds, Carlos E. Cintra-Buenrostro

School of Earth, Environmental, & Marine Sciences Faculty Publications

The analysis of predatory drillholes allow paleontologists to reconstruct trophic relationships of ancient systems. To evaluate the potential effects of climate and sea level change on predation frequency by gastropods on bivalves, species of the genus Chione from the Gulf of California were selected because they are a commercially exploited resource - at least locally - and abundant in both modern and Pleistocene (sea level high stand of oxygen substage 5e) samples from rhodolith beds. The present study focused to answer a practical question: would predation on Chione spp. increase under the suggested climate - warming - change scenario? A …

Selective Capture Of Transcribed Sequences: A Promising Approach For Investigating Bacterium-Insect Interactions, Ruisheng An, Parwinder Grewal

School of Earth, Environmental, & Marine Sciences Faculty Publications

Bacterial interactions with eukaryotic hosts are complex processes which vary from pathogenic to mutualistic. Identification of bacterial genes differentially expressed in the host, promises to unravel molecular mechanisms driving and maintaining such interactions. Several techniques have been developed in the past 20 years to investigate bacterial gene expression within their hosts. The most commonly used techniques include in-vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays. However, the limitations of these techniques in analyzing bacterial in-vivo gene expression indicate the need to develop alternative tools. With many advantages over the other methods for analyzing bacterial in-vivo gene expression, …

Extensive Reproductive Disruption, Ovarian Masculinization And Aromatase Suppression In Atlantic Croaker In The Northern Gulf Of Mexico Hypoxic Zone, Peter Thomas, Md. Saydur Rahman

School of Earth, Environmental, & Marine Sciences Faculty Publications

The long-term impacts on marine ecosystems of the recent dramatic worldwide increase in the incidence of coastal hypoxia are unknown. Here, we show widespread reproductive disruption in Atlantic croakers collected from hypoxic sites approximately 120 km apart in the extensive northern Gulf of Mexico continental shelf hypoxic zone. Gonadal growth and gamete production were impaired in croakers from hypoxic sites compared with fish from reference normoxic sites east of the Mississippi River Delta. Male germ cells were detected in approximately 19 per cent of croaker ovaries collected in the hypoxic region, but were absent in ovaries from normoxic sites. In …

Would Predatory Drillhole Frequency On Chione Spp. Increase Under The Suggested Climate Change Scenario? Comparing Pleistocene And Modern Rhodolith Beds, Carlos E. Cintra-Buenrostro

School of Earth, Environmental, & Marine Sciences Faculty Publications

The analysis of predatory drillholes allow paleontologists to reconstruct trophic relationships of ancient systems. To evaluate the potential effects of climate and sea level change on predation frequency by gastropods on bivalves, species of the genus Chione from the Gulf of California were selected because they are a commercially exploited resource - at least locally - and abundant in both modern and Pleistocene (sea level high stand of oxygen substage 5e) samples from rhodolith beds. The present study focused to answer a practical question: would predation on Chione spp. increase under the suggested climate - warming - change scenario? A …

Stability Of Rock Slopes Along Raidah Escarpment Road, Asir Area, Kingdom Of Saudi Arabia, Ahmed M. Youssef, Norbert H. Maerz, Abdulla A. Al-Otaibi

Geosciences and Geological and Petroleum Engineering Faculty Research & Creative Works

The Raidah Escarpment road is located north west of Abha city, Asir region, Kingdom of Saudi Arabia. This escarpment road represents an important corridor in the area which connects different villages and tourist resorts with each other. The total length of this road section is about 9 km which passes through a highly mountainous area. The road also passes through areas of different geological hazards (rock, debris flow, soil, and weathered zones). The different environmental factors (e.g. intensive rainy summer), variable geological and structural elements (weak rocks, slide debris weak soils, shear zones, and faults) difficult road characteristics (narrow roads …

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 …

Quantitative Field Testing Rotylenchulus Reniformis Dna From Metagenomic Samples Isolated Directly From Soil., Kurt Showmaker, Gary W. Lawrence, Shien Lu, Clarissa Balbalian, Vincent P. Klink

CALS Publications

A quantitative PCR procedure targeting the ?-tubulin gene determined the number of Rotylenchulus reniformis Linford & Oliveira 1940 in metagenomic DNA samples isolated from soil. Of note, this outcome was in the presence of other soil-dwelling plant parasitic nematodes including its sister genus Helicotylenchus Steiner, 1945. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from soil.

Surface Water Characteristics Of The Weaber Plain And Lower Keep River Catchments: Data Review And Preliminary Results, D L. Bennett, Richard J. George Dr

Resource management technical reports

In 2008, the Ord Irrigation Expansion Project was approved by the Western Australian Government to develop irrigated agriculture on the Weaber Plain.

An important concern is the effect the Weaber Plain agricultural development may have on the water quality of the downstream Border Creek and Keep River

This report assembles and reviews all available physico-chemical water quality data for the lower Keep River and Border Creek systems and presents data from the initial year of a targeted baseline monitoring program (June 2010 – June 2013).

Land Systems Of The Kimberley Region, Western Australia, A L. Payne, N Schoknecht

Technical Bulletins

The Land Systems of the Kimberley Region Report describes and maps the landscapes, soils and vegetation of the Kimberley region. This report is a consolidation of surveys carried out by different organisations, across different areas of the Kimberley, since the 1940s. The Kimberley region, as defined in this bulletin, covers 330 070km². The report categorises the Kimberley region into 111 land systems. Under each land system, the report identifies the vulnerabilities of those areas, and provides recommendations on how to achieve sustainable use. The report also publishes pasture types for the entire region and the grazing potential for each pasture, …

Multiple Storm Event Impacts On Epikarst Storage And Transport Of Organic Soil Amendments In South-Central Kentucky, Sean M. Vanderhoff

Masters Theses & Specialist Projects

The groundwater in agricultural karst areas is susceptible to contamination from organic soil amendments and pesticides. During major storm events during 2011, dye traces were initiated using sulphorhodamine-B, fluorescein and eosine in a groundwater recharge area where manure was applied to the ground. Fecal coliform samples were collected from significant storm events from January-September 2011. Water samples and geochemical data were collected every four hours before, during, and between the storm events from a waterfall in Crumps cave flowing from the known recharge area to track the transport and residence time of the epikarst water and organic soil amendments during …

Three-Dimensionally Preserved Integument Reveals Hydrodynamic Adaptations In The Extinct Marine Lizard Ectenosaurus (Reptilia, Mosasauridae), Johan Lindgren, Michael J. Everhart, Michael W. Caldwell

Sternberg Museum of Natural History Faculty Publications

The physical properties of water and the environment it presents to its inhabitants provide stringent constraints and selection pressures affecting aquatic adaptation and evolution. Mosasaurs (a group of secondarily aquatic reptiles that occupied a broad array of predatory niches in the Cretaceous marine ecosystems about 98-65 million years ago) have traditionally been considered as anguilliform locomotors capable only of generating short bursts of speed during brief ambush pursuits. Here we report on an exceptionally preserved, long-snouted mosasaur (Ectenosaurus clidastoides) from the Santonian (Upper Cretaceous) part of the Smoky Hill Chalk Member of the Niobrara Formation in western Kansas, USA, that …

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 …

Age, Stratigraphy And Depositional Environment Of The Pliocene Copper Canyon Formation, Death Valley, California, Torrey Nyborg

Loma Linda University Electronic Theses, Dissertations & Projects

The Copper Canyon Formation, a fluvial-lacustrine deposit exposed within the Black Mountains of Death Valley National Park, has only previously been broadly included in regional tectonic and depositional analyses. The formation is significant because it preserves numerous shoreline-playa features including highly abundant and diverse mammal and bird tracks. The formation represents a basin fill sequence consisting of approximately 1800 m of conglomerates, basalt flows, and lacustrine deposits. A measured type section along with x-ray diffraction, isotopic analysis, and thin section petrography shows an evolution of the ancient Copper Canyon lake from an hypersaline evaporative lake to a perennial saline lake …

Using Geographical Information Systems To Investigate Spatial Patterns In Fossils Of Tapirus Polkenis From The Gray Fossil Site, Washington County, Tennessee, Winn Addison Ketchum

Electronic Theses and Dissertations

Discovered in 2000, the Gray Fossil Site provides a snapshot of the flora and fauna that lived during late Miocene to early Pliocene time in eastern Tennessee. These fossils occur in sediments consisting of fine-grained clays and sands of lacustrine origin, which were deposited after multiple sinkholes formed in the underlying Knox Group basement carbonates. Three-dimensional nearest neighbor analysis has been applied to fossils of Tapirus polkensis, characterizing the spatial patterns exhibited. These analyses determined the importance of taphonomic and depositional processes that occurred during the sites formation. Six characteristics were analyzed, four at the bone level including carnivore …