Digital Commons Network^™

Phyr: Anrpackage For Phylogenetic Species-Distribution Modelling In Ecological Communities, Daijiang Li, Russell Dinnage, Lucas A. Nell, Matthew R. Helmus, Anthony Ives

Faculty Publications

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to a lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily. To fill this gap, therpackagephyr(pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other …

Great Lakes Snake: Estimating The Occupancy And Detection Probabilities Of The Eastern Massasauga Rattlesnake (Sistrurus Catenatus), Arin June Thacker

Masters Theses

Detailed knowledge of a species’ range and distribution is important for understanding species persistence and developing species management plans. This issue is particularly pronounced in threatened species with wide-spread range and a low detectability in their natural environment, as surveying and successfully encountering this type of species is oftentimes difficult. One such species is the eastern massasauga rattlesnake (Sistrurus catenatus), a smallbodied pit viper with a distribution centered around the Great Lakes region. We used singleseason occupancy modeling in order to reassess the status of historic massasauga occurrences. We evaluated factors affecting eastern massasauga detection probability from a …

Experimental Nitrogen Addition Alters Structure And Function Of A Boreal Poor Fen: Implications For Critical Loads, R. Kelman Wieder, Dale H. Vitt, Melanie A. Vile, Jeremy A. Graham, Jeremy A. Hartsock, Jacqueline M.A. Popma, Hope Fillingim, Melissa House, James C. Quinn, Kimberli D. Scott, Meaghan Petix, Kelly J. Mcmillen

Public Health Sciences Faculty Publications

Bogs and fens cover 6 and 21%, respectively, of the 140,329 km2 Oil Sands Administrative Area in northern Alberta. Regional background atmospheric N deposition is low (b2 kg N ha−1 yr−1 ), but oil sands development has led to increasing N deposition (as high as 17 kg N ha−1 yr−1 ). To examine responses to N deposition, over five years, we experimentally applied N (as NH4NO3) to a poor fen near Mariana Lake, Alberta, unaffected by oil sands activities, at rates of 0, 5, 10, 15, 20, and 25 kg N ha−1 yr−1 , plus controls (no water or N …

College Of Natural Sciences Newsletter, September 2020, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Issue 1. Volume 8

Contents:

Dean’s Update P.1
Awards & Recognition P.2
Interest in Science | Competitions P.3
Open PRAIRIE | ODFS Recap P.4
ODFS Recap | Research Spotlight P.5
Spring 2020 Dean’s List P.6-7

Defining Relictual Biodiversity: Conservation Units In Speckled Dace (Leuciscidae: Rhinichthys Osculus) Of The Greater Death Valley Ecosystem, Steven M. Mussmann, Marlis R. Douglas, David D. Oakey, Michael E. Douglas

Biological Sciences Faculty Publications and Presentations

The tips in the tree of life serve as foci for conservation and management, yet clear delimitations are masked by inherent variance at the species–population interface. Analyses using thousands of nuclear loci can potentially sort inconsistencies, yet standard categories applied to this parsing are themselves potentially conflicting and/or subjective [e.g., DPS (distinct population segments); DUs (Diagnosable Units-Canada); MUs (management units); SSP (subspecies); ESUs (Evolutionarily Significant Units); and UIEUs (uniquely identified evolutionary units)]. One potential solution for consistent categorization is to create a comparative framework by accumulating statistical results from independent studies and evaluating congruence among data sets. Our study illustrates …

Biosecurity Council Of Western Australia Annual Report 2019/2020, Biosecurity Council Of Western Australia

Biosecurity published reports

In order to develop constructive advice, it is important for the Biosecurity Council to understand the needs and challenges of industry, government and the community, and how changes to the biosecurity system might impact these groups. During 2019/20 the Council continued to monitor biosecurity-related developments at national and State levels and proactively engaged with industry, community and government on biosecurity matters.

The key areas of advice that were progressed during the year were:

• biosecurity research and development
• border biosecurity
• the declaration of non-agricultural pests under the BAM Act; and
• recognised biosecurity groups and declared pest rates

Challenging The Wallacean Shortfall: A Total Assessment Of Insect Diversity On Guadeloupe (French West Indies), A Checklist And Bibliography, François Meurgey, Thibault Ramage

Insecta Mundi

This work is the first attempt to integrate into one list and quantify all the known species of Guade­loupean insects. It includes all the species known to us to be reported for the island of Guadeloupe until the 31^st of December 2019. A total of 3097 valid species are listed, of which the largest component is the beetles (1447 species). Preliminarily, 632 species (20%) are considered to be strictly endemic to Guadeloupe, and 250 species are recognized as adventive or introduced. The bibliography complements the taxonomic information and includes over 350 titles. Brief annotations are also given on the …

The Roles Of Host Species, Geographic Scale And Environmental Stressors In Shaping The Composition Of Coral Microbiomes, Alicia Marie Riegel Parker

LSU Doctoral Dissertations

Reef-building corals are long-lived and may take many centuries to adapt, making them especially susceptible to climate change. However, corals host microbial symbionts that can change quickly, potentially speeding acclimation. My dissertation aimed to determine the degree of coevolution and flexibility between corals and their microbiomes among hosts, across space, and in response to stress.

Microbial communities are usually surveyed by sequencing the 16S rRNA gene, however the PCR primers used also amplify coral DNA, thereby limiting prokaryotic read coverage. To mitigate this contamination, I designed a peptide nucleic acid clamp that increased the recovery of bacterial reads by 2-11x …

Patterns For Populus Spp. Stand Biomass In Gradients Of Winter Temperature And Precipitation Of Eurasia, Vladimir Andreevich Usoltev, Baozhang Chen, Seyed Omid Reza Shobairi, Ivan Stepanovich Tsepordey, Viktor Petrovich Chasovskikh, Shoaib Ahmad Anees

Aspen Bibliography

Based on a generated database of 413 sample plots, with definitions of stand biomass of the genus Populus spp. in Eurasia, from France to Japan and southern China, statistically significant changes in the structure of forest stand biomass were found, with shifts in winter temperatures and average annual precipitation. When analyzing the reaction of the structure of the biomass of the genus Populus to temperature and precipitation in their transcontinental gradients, a clearly expressed positive relationship of all components of the biomass with the temperature in January is visible. Their relationship with precipitation is less clear; in warm climate zones, …

A Mechanistic And Genomic Analysis Of Molluscum Contagiosum Virus Immune Evasion, Ian Benjamin Harvey

Arts & Sciences Graduate Student Theses and Dissertations

Molluscum contagiosum virus (MCV) is a common human-specific poxvirus with a proclivity forinfecting children and the immune-compromised. A characteristic MCV infection is restricted tothe epidermal layers of the skin and can persist for weeks to years in an otherwise healthyindividual. The high clinical burden of MCV is at odds with our limited knowledge regarding howit successfully evades the human immune response, which is in part due to the lack of an animalmodel or cell line to propagate the virus. Through this dissertation, we have uncovered andcharacterized a novel mechanism by which MC80, a protein encoded by MCV, downregulateshost MHC-I surface …

Genomic Analysis Of Diverse Bacterial Pathogens, Robert Potter

Arts & Sciences Graduate Student Theses and Dissertations

Bacterial pathogens have been a historical scourge for the entirety of human existence but have been significantly thwarted since the 20th century due to the development of antibiotics. However, owing to the large selection pressure of antibiotics on bacterial populations, phenotypic antibiotic resistance from the development of vertically transmitted mutations and horizontally acquired antibiotic resistance genes (ARGs) is increasing. The sum has produced multidrug resistant organisms (MDROs) which have extremely limited treatment options. Epidemiological studies have determined that carbapenem resistant Enterobacteriaceae (CRE), Acinetobacter baumannii, and vancomycin resistant Enterococcus (VRE) are some of the most problematic MDRO infections. The advent of …

Pathophysiology And Proteogenomics Of Post-Infectious And Post-Hemorrhagic Hydrocephalus In Infants, Albert M. Isaacs

Arts & Sciences Graduate Student Theses and Dissertations

Post-infectious (PIH) and post-hemorrhagic (PHH) hydrocephalus occur as sequalae of neonatal sepsis or intraventricular hemorrhage (IVH) of prematurity, respectively. Together, PIH and PHH represent the most common form of infantile hydrocephalus, the most common indication for neurosurgery in children globally, and the leading cause of neurological morbidity and mortality worldwide. The lack of understanding of the pathophysiology of PIH and PHH, particularly with regards to the host central nervous system response to the antecedent infection and hemorrhage, perturbation of differentiating neural stems in the ventricular (VZ) and subventricular (SVZ) zones, and damage to periventricular white matter (PVWM) tracts carrying sensorimotor …

Do Ground Layer Microhabitats In Old-Growth Pine Savanna Influence Recruitment Of Longleaf Pine?, Matthew Blanchard

LSU Master's Theses

Savanna tree populations typically share two demographic characteristics, high mortality of juvenile stages and low mortality of established trees. Juvenile savanna tree species escape demographic bottlenecks when they reach a safe size and annual mortality becomes low. Longleaf pine (Pinus palustris Mill.) is the dominant tree species in pine savannas of the southeastern United States. The seeds and juvenile seedlings experience bottlenecks to recruitment to a safe size, the grass stage. Low intensity, frequent savanna fires facilitate establishment of seedlings, but also kill juvenile seedlings that have not grown sufficient above ground biomass. We hypothesized that juvenile seedlings escape the …

Exploring The Effects Of Geographic And Landscape Variation On Avian Communities And Species, Joseph Youtz

Student Theses and Dissertations

Ongoing and intensive anthropogenic change has modified the globe across multiple scales, yet the influence of these modifications on wildlife communities and individuals remain region and species specific. Here I explored the influence of a biogeographical pattern as it relates to climate and geography, and the effects of historic habitat loss and fragmentation on a diverse avian community. I first explored the adherence to Bergmann’s rule within a migratory songbird, the Prothonotary Warbler (Protonotaria citrea), across all life stages and time. The pattern was present from the young nestling stage through adulthood, although contemporary eggs followed a reverse relationship with …

Integrative Species Delimitation And Taxonomic Status Of The Scorpion Genus Vaejovis Koch, 1836 (Vaejovidae) In The Santa Catalina Mountains, Arizona, Emma E. Jochim, Lillian-Lee M. Broussard, Brent E. Hendrixson

Euscorpius

Scorpions belonging to the Vaejovis vorhiesi species complex are widely distributed throughout the southwestern United States and northern Mexico. Most species are endemic to single mountain ranges but two species, Vaejovis deboerae Ayrey, 2009 and V. brysoni Ayrey & Webber, 2013, have been documented from the Santa Catalina Mountains in Arizona. We reevaluated the taxonomic diversity of these scorpions by integrating data from several different sources. Phylogenetic analyses indicate that scorpions in the Santa Catalina Mountains are monophyletic but comprise two divergent mitochondrial lineages that overlap at the type locality of V. deboerae. We failed to detect congruence between …

Snow-Albedo Feedback In Northern Alaska: How Vegetation Influences Snowmelt, Lucas C. Reckhaus

Theses and Dissertations

This paper investigates how the snow-albedo feedback mechanism of the arctic is changing in response to rising climate temperatures. Specifically, the interplay of vegetation and snowmelt, and how these two variables can be correlated. This has the potential to refine climate modelling of the spring transition season. Research was conducted at the ecoregion scale in northern Alaska from 2000 to 2020. Each ecoregion is defined by distinct topographic and ecological conditions, allowing for meaningful contrast between the patterns of spring albedo transition across surface conditions and vegetation types. The five most northerly ecoregions of Alaska are chosen as they encompass …

Assessing The Potential For Range Expansion Of The Red Tide Algae Karenia Brevis, Edward W. Young

All HCAS Student Capstones, Theses, and Dissertations

Phytoplankton communities are vital to oceanic ecosystems. While most are harmless or beneficial, a select group possesses the capability to produce toxins and cause mass die-offs of marine organisms. Florida red tide, caused by blooms of the dinoflagellate Karenia brevis, is common in the Gulf of Mexico, although blooms have been transported to the Atlantic coast and impacted estuaries where K. brevis is not normally found. An in-depth overview of compiled estuary research evaluated the possibility of the continued spread of Florida red tide blooms to Southeastern Atlantic estuaries and the likelihood of establishment in non-native regions. A …

Potential Of Resampled Multispectral Data For Detecting Desmodium-Brachiaria Intercropped With Maize In A 'Push-Pull' System, B. T. Mudereri, E. M. Abdel-Rahman, T. Dube, T. Landmann, S. Niassy, H. E.Z. Tonnang, Z. R. Khan

All Peer-Reviewed Publications

Poor crop yields remain one of the main causes of chronic food insecurity in Africa. This is largely caused by insect pests, weeds, unfavourable climatic conditions and degraded soils. Weed and pest control, based on the climate-adapted g'push-pull' system, has become an important target for sustainable intensification of food production adopted by many small-holder farmers. However, essential baseline information using remotely sensed data is missing, specifically for the g'push-pull' companion crops. In this study, we investigated the spectral uniqueness of two of the most commonly used g'companion' crops (i.e. greenleaf Desmodium (i Desmodium intortum/i) and Brachiaria (i Brachiaria/i cv Mulato) …

Herbivores At The Highest Risk Of Extinction Among Mammals, Birds, And Reptiles, Trisha B. Atwood, Shaley A. Valentine, Edd Hammill, Douglas J. Mccauley, Elizabeth M. P. Madin, Karen H. Beard, William D. Pearse

Ecology Center Publications

As a result of their extensive home ranges and slow population growth rates, predators have often been perceived to suffer higher risks of extinction than other trophic groups. Our study challenges this extinction-risk paradigm by quantitatively comparing patterns of extinction risk across different trophic groups of mammals, birds, and reptiles. We found that trophic level and body size were significant factors that influenced extinction risk in all taxa. At multiple spatial and temporal scales, herbivores, especially herbivorous reptiles and large-bodied herbivores, consistently have the highest proportions of threatened species. This observed elevated extinction risk for herbivores is ecologically consequential, given …

Stream Biodiversity And Co-Occurrence Network Topology Along Sub-Continental To Global Nutrient And Land Use Gradients, William Robert Budnick

Biology Dissertations - Archive

Freshwaters are some of the most vulnerable ecosystems to global change forces, such as land use and eutrophication, implicated in the loss of biodiversity and biotic homogenization (increased similarity) of species communities. However, much less is known about the impact of these forces on the mechanisms underlying biodiversity and the patterns of species co-occurrence. In this dissertation, I use sub-continental to global stream community datasets to investigate the effects of land use and nutrients on algal, macroinvertebrate, and fish biodiversity, abundance, and complexity of co-occurrence patterns to pursue three objectives. I first investigate how agriculture contributes to biotic homogenization, and …

Patterns And Drivers In Counts Of Migratory Raptors At Hawk Mountain Sanctuary, Usa, Patricia Kaye Tahura Dumandan

Boise State University Theses and Dissertations

Understanding the mechanisms driving biodiversity patterns amidst an era of global environmental change is the core of modern ecological research. The magnitude of biodiversity losses associated with anthropogenic activities has prompted resource managers and ecologists alike to identify strategies to address conservation issues. Broadly, two types of approaches are employed to answer ecological research questions: 1) single-species and 2) ecosystem-based approach. Single-species approaches are often useful to elucidate mechanisms driving population trajectories of individual species. On the other hand, ecosystem-based approaches can help in identifying general patterns that may be useful for multi-species management.

Here, I used both approaches in …

The Assessment Of Co2 Exposures, Workload Demands, And Musculoskeletal Disorder Risk On Heart Rate For Select Craft Brewery Job Tasks, David L. Huizen

Dissertations

Americans have embraced craft beer, and the ensuing demand has resulted in an ever-increasing number of craft breweries opening over the past 20 years. Craft brewers are generally small employers and, as such, lack the resources necessary to address the safety and health of their employees adequately. Brewers face many safety and health hazards in their work environment. These hazards include exposures to carbon dioxide (CO₂), workload demand, and MSD risk. It is essential to evaluate these hazards in craft breweries as they handle carbon dioxide (CO₂) differently than large breweries by having the CO_{2 …}

College Of Natural Sciences Newsletter, August 2020, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Volume 1. Issue 7

Contents:

Dean’s Update P.1
Awards & Recognition P.2
New Faculty | Student Clubs P.3
Research Spotlight | Open PRAIRIE P.4
ODFS | Interest in Science P.3

Adapting Biotoxin Monitoring For The Future: An Opportunity For A Harmful Algae Bloom (Hab) Network In Casco Bay, Maine, Zachary B. Gordon

All Theses And Dissertations

Harmful Algae Blooms (HABs) related to marine biotoxins have considerable impacts on coastal communities and have been increasing in size and frequency globally. Maine is recognized as a leader in biotoxin management as it relates to bivalve shellfish, but it has been unclear how current management practices effect the growth of shellfish aquaculture and how they will adapt to future conditions. This research uses a collaborative approach to analyze the current state of biotoxin management in Maine. First, the current management practices in Maine were compared and contrasted with five other states dealing with similar issues. Then, the perspectives of …

Plant Science Decadal Vision 2020–2030: Reimagining The Potential Of Plants For A Healthy And Sustainable Future, Natalie Henkhaus, Madelaine Bartlett, David Gang, Rebecca Grumet, Ingrid Jordon‐Thaden, Argelia Lorence, Eric Lyons, Samantha Miller, Seth Murray, Andrew Nelson, Chelsea Specht, Brett Tyler, Thomas Wentworth, David Ackerly, David Baltensperger, Philip Benfey, James Birchler, Sreekala Chellamma, Roslyn Crowder, Michael Donoghue, Jose Pablo Dundore‐Arias, Jacqueline Fletcher, Valerie Fraser, Kelly Gillespie, Lonnie Guralnick, Elizabeth Haswell, Mitchell Hunter, Shawn Kaeppler, Stefan Kepinski, Fay‐Wei Li, Sally Mackenzie, Lucinda Mcdade, David Stern

Arkansas Biosciences Institute

Plants, and the biological systems around them, are key to the future health of the planet and its inhabitants. The Plant Science Decadal Vision 2020–2030 frames our ability to perform vital and far-reaching research in plant systems sciences, essential to how we value participants and apply emerging technologies. We outline a comprehensive vision for addressing some of our most pressing global problems through discovery, practical applications, and education. The Decadal Vision was developed by the participants at the Plant Summit 2019, a community event organized by the Plant Science Research Network. The Decadal Vision describes a holistic vision for the …

Plasmodium Impairs Antibacterial Innate Immunity To Systemic Infections In Part Through Hemozoin-Bound Bioactive Molecules., Christopher Lynn Harding

Electronic Theses and Dissertations

Despite efforts to decrease the global health burden of malaria, infections with Plasmodium species continue to cause over 200 million episodes of malaria each year which resulted in 405,000 deaths in 2018 [1]. One complication of malaria is increased susceptibility to invasive bacterial infections. Plasmodium infections impair host immunity to non-Typhoid Salmonella (NTS) through activities of heme oxygenase I (HO-I) )-induced release of immature granulocytes and myeloid cell-derived IL-10. Yet, it is not known if these mechanisms are specific to NTS. We show here, that Plasmodium yoelii 17XNL (Py) infected mice had impaired clearance of systemic Listeria monocytogenes (Lm) during …

Analysis Of The Role Of Dnaa Recognition Site Position In Directing Assembly Of The Pre-Replicative Complex In Escherichia Coli, Christopher Aaron Czerwonka

Theses and Dissertations

Prior to initiating new rounds of DNA replication, all cells assemble pre-replicative complexes (pre-RC) consisting of initiator proteins and regions of DNA termed origins of replication. In the bacterial model system, E. coli, multiple copies of the initiator protein, DnaA,assemble into a complex with the unique chromosomal replication origin, oriC, to produce a pre-RC that unwinds the DNA helix, preparing the origin for the new replication forks. Nine base pair (bp) low affinity DnaA recognition sites are distinctly arrayed in each half of oriC and both arrays are bounded by high affinity recognition sites. Although it is known that DnaA …

Estimation Of Wildlife Damage From Federal Crop Insurance Data, Sophie Mckee, Stephanie A. Shwiff, Aaron M. Anderson

United States Department of Agriculture Wildlife Services: Staff Publications

BACKGROUND: Wildlife damage to crops is a persistent and costly problem for many farmers in the USA. Most existing estimates of crop damage have relied on direct assessment methods such as field studies conducted by trained biologists or surveys distributed to farmers. In this paper, we describe a new method of estimating wildlife damage that exploits federal crop insurance data. We focused our study on four crops: corn, soybean, wheat, and cotton, chosen because of their economic importance and their vulnerability to wildlife damage.

RESULTS: We determined crop-raiding hot spots across the USA over the 2015–2019 period and identified the …

Geology, Soils And Climate Of The Margaret River Wine Region, Peter J. Tille, Angela Stuart-Street, Peter S. Gardiner

All other publications

This report is an extract from the broader description and analysis of the Geology, soils and climate of Western Australia's wine regions. It expands on the brief descriptions in the second edition of 'Viticulture' (Coombe & Dry 2004) concerning the soils and landscapes of Western Australia’s main wine growing regions. We have tailored this report extract to the specific needs of the Margaret River wine region. It contains local soil names and soil-landscape zones and systems maps.

The wine industry recognises the importance of giving customers an understanding of the vines’ environment and how that may influence wine character …

Boracay Island Destination Image Through Travel Blogs, Peter Lorenz Salmon, Ronelia Amen, Jan Patrick Aguilar, John Benedict Javellana, Cheryl Joy Fernandez

Journal of Environmental Science and Sustainable Development

Destination images are important information for marketing professionals, local planners, and travel bloggers on social media. The rise of social media has allowed more tourists to share their knowledge, emotions, and experiences from their travels. However, despite the popularity of adapting online narratives to destination images, little or no qualitative analysis has been conducted about island’s sustainable tourism development in the Philippines using information from social media. One type of destination are small islands in the Philippines. The examination is worthwhile inasmuch as the literature has been silent on destination images of top island retreats in the country, although there …