Digital Commons Network^™

Coproid Predicts The Source Of Coprolites And Paleofeces Using Microbiome Composition And Host Dna Content, Maxime Borry, Bryan Cordova, Angela Perri, Marsha Wibowo, Tanvi Prasad Honap, Jada Ko, Kate Britton, Linus Girdland-Flink, Robert C. Power, Ingelise Stuijts, Domingo C. Salazar-García, Courtney Hofman, Richard Hagan, Thérèse Samdapawindé Kagoné, Nicolas Meda, Helene Carabin, David Jacobson, Karl Reinhard, Cecil Lewis, Aleksandar Kostic, Choongwon Jeong, Alexander Herbig, Alexander Hübner, Christina Warinner

Karl Reinhard Publications

Shotgun metagenomics applied to archaeological feces (paleofeces) can bring new insights into the composition and functions of human and animal gut microbiota from the past. However, paleofeces often undergo physical distortions in archaeological sediments, making their source species difficult to identify on the basis of fecal morphology or microscopic features alone. Here we present a reproducible and scalable pipeline using both host and microbial DNA to infer the host source of fecal material. We apply this pipeline to newly sequenced archaeological specimens and show that we are able to distinguish morphologically similar human and canine paleofeces, as well as non-fecal …

Patterns Of Genetic Diversity In Highly Invasive Species: Cogongrass (Imperata Cylindrica) Expansion In The Invaded Range Of The Southern United States (Us), Rima D. Lucardi, Lisa E. Wallace, Gary N. Ervin

Biological Sciences Faculty Publications

The spatial expansions of invasive organisms in the novel range are generally expected to follow an isolation-by-distance relationship (IBD) if the invasion is biologically driven; however, many invasions are facilitated anthropogenically. This research focused on the extant expansion patterns of cogongrass (Imperata cylindrica). Cogongrass is a widespread invasive species throughout the southern United States (US). Patterns of infestation vary among US states. Cogongrass is pyrogenic, and its invasion threatens softwood (Pinus spp.) plantations, a substantial economic market for this US region. Over 600 individuals were sampled from seven invaded US states, using amplified fragment length polymorphisms (AFLPs) …

A Survey Of The Reptiles And Amphibians At The University Of Georgia Costa Rica Field Station In San Luis De Monteverde, Costa Rica, John David Curlis, Elliot Convery Fisher, W. Kody Muhic, James Moy, Martha Garro-Cruz, José Joaquín Montero-Ramírez

Biological Sciences Faculty Publications

Reptiles and amphibians are experiencing declines across the globe. In Monteverde, Costa Rica, these declines and their underlying causes have been relatively well studied since the early 1990s, and many protected areas have been set aside to conserve these species. However, thorough surveys of the herpetofaunal diversity in these areas have been scarce over the last 20 years. We conducted a survey of all reptile and amphibian species at the University of Georgia Costa Rica (UGACR), a field station in San Luis de Monteverde. Herein, we present an annotated checklist of the 48 species (35 reptiles and 13 amphibians) that …

Environmental Governance For Whom? Examining The Political, Institutional, Fiscal, And Legal Determinants Of State Environmental Agency Budget Policy In The Us, Andrew R. Duggan

Theses and Dissertations

Budgets are a prospective tool of governance, and appropriations are a planning vehicle reflecting: bureaucracies’ values, complex interactions, collective preferences, political influences, and available resources. Research spanning 30 years finds that environmental pollution is a key determinant of environmental budgets in the US, though myriad factors, actors, and subsystems are important to consider. Due to federalism and devolution of responsibilities and authorities, environmental governance falls largely to the states. While the dynamics that shape state environmental budget policy have received scholarly interest, theoretically-driven examinations of environmental appropriations remain limited within the public budgeting and environmental policy literature.

Using panel data …

Impacts Of Vegetation Density And Distance From The High Tide Line On Raccoon Predation Of Diamondback Terrapin Nests In Jamaica Bay, Ny – A Preliminary Study, Zvi Teitelbaum

Dissertations and Theses

Diamondback terrapin turtles (Malaclemys terrapin) have been culturally and economically important since at least the nineteenth century. However, due to overharvesting, this became a species of conservation concern. While extensive data are available to describe its natural history, some conditions that impact nest predation are poorly understood. In this exploratory study, vegetation type and distance to the high tide line were examined to determine their potential impact on predation of diamondback terrapin nests by raccoons. For that, terrapin scented water was used to construct 50 artificial nests at Jamaica Bay Wildlife Refuge. These artificial nests were placed in …

Stone-Stacking As A Looming Threat To Rock-Dwelling Biodiversity, Ricardo Rocha, Paulo A. V. Borges, Pedro Cardoso, Mirza Dikari Kusrini, José Luis Martín-Esquivel, Dília Menezes, Mário Mota-Ferreira, Sara F. Nunes, Inês Órfão, Catarina Serra-Gonçalves, Manuela Sim-Sim, Pedro Sepúlveda, Dinarte Teixeira, Anna Traveset

Human–Wildlife Interactions

This letter to the editor describes the surge of “photo-friendly” stacks of stones as an emerging tourism-associated threat to rock-dwelling biodiversity.

Interspecific Gene Flow Potentiates Adaptive Evolution In A Hybrid Zone Formed Between Pinus Strobiformis And Pinus Flexilis, Mitra Menon

Theses and Dissertations

Species range margins are often characterised by high degrees of habitat fragmentation resulting in low genetic diversity and higher gene flow from populations at the core of the species range. Interspecific gene flow from a closely related species with abutting range margins can increase standing genetic diversity and generate novel allelic combinations thereby alleviating limits to adaptive evolution in range margin populations. Hybridization driven interspecific gene flow has played a key role in the demographic history of several conifer due to their life history characteristics such as weak crossability barriers and long generation times. Nevertheless, demonstrating whether introgression is adaptive …

Variation Of Symbiodiniaceae In Broadcaster Acropora Humilis And Brooder Pocillopora Damicornis Corals, Suppakarn Jandang

Chulalongkorn University Theses and Dissertations (Chula ETD)

Reef-building corals sustain a symbiotic relationship with single-cell algae belonging to family Symbiodiniaceae. Symbiotic algae contribute up to 50-95% of the metabolic needs by supplying photosynthetic products to the coral host. Therefore, the symbiosis between corals and Symbiodiniaceae is essential for the development and survival of coral reefs. Over the past years, significant losses and changes in coral reef ecosystems have been caused by anthropogenic activities and natural phenomena. Thus, relevant national organizations have raised awareness regarding the conservation of coral populations. Our Reef Biology Research Group, Department of Marine Science, Chulalongkorn University have been producing corals using a sexual …

Gonadal Sex Differentiation Of Rice Field Frog Hoplobatrachus Rugulosus (Wiegmann, 1834), Thrissawan Traijitt

Chulalongkorn University Theses and Dissertations (Chula ETD)

The rice field frog Hoplobatrachus rugulosus, a species widely distributed in Thailand, has potential to be a model in many fields of research. A preliminary study demonstrated that the gonadal differentiation in this frog showed tendency to be an undifferentiated type since all individuals had ovaries at complete metamorphosis. However, the information was still unclear. Therefore, this study aimed to investigate the chronology and pattern of gonadal sex differentiation as well as steroidogenic potential of gonadal tissues during development. The frog embryos were obtained by stimulating fertilization in laboratory under natural light and temperature conditions. Their developmental stage was identified …

First Report Of Molecular Characterization And Phylogeny Of Trichuris Fossor Hall, 1916 (Nematoda: Trichuridae), Malorri R. Hughes, Deborah A. Duffield, Dana K. Howe, Dee Denver

Biology Faculty Publications and Presentations

Because species of Trichuris are morphologically similar and ranges of host preference are variable, using molecular data to evaluate species delineations is essential for properly quantifying biodiversity of and relationships within Trichuridae. Trichuris fossor has been reported from Thomomys spp. (Rodentia: Geomyidae, ‘pocket gophers’) hosts based on morphological features alone. Partial 18S rRNA sequences for specimens identified as T. fossor based on morphology, along with sequences from 26 additional taxa, were used for a phylogenetic analysis. Evolutionary histories were constructed using maximum likelihood and Bayesian inference. In both analyses, the specimens fell within the Trichuris clade with 100% support and …

Crossing Boundaries: Steps Toward Measuring Undergraduates' Interdisciplinary Science Understanding, Brie Tripp, Sophia A. Voronoff, Erin Shortlidge

Biology Faculty Publications and Presentations

A desired outcome of education reform efforts is for undergraduates to effectively integrate knowledge across disciplines in order to evaluate and address real-world issues. Yet there are few assessments designed to measure if and how students think interdisciplinarily. Here, a sample of science faculty were surveyed to understand how they currently assess students’ interdisciplinary science understanding. Results indicate that individual writing-intensive activities are the most frequently used assessment type (69%). To understand how writing assignments can accurately assess students’ ability to think interdisciplinarily, we used a preexisting rubric, designed to measure social science students’ interdisciplinary understanding, to assess writing assignments …

Inhibition Of Glycine Transporter 2: An Emerging Target For Chronic Pain, Elvia Lilia Padilla

Open Access Theses & Dissertations

Chronic pain is a complicated, completely unknown condition that has been studied based on its severe impact on the population. According to the American Academy of Pain Medicine, 1.5 billion people suffer from tension-type headaches, one of the most common symptomatic chronic conditions. Christopher L. Cioffi, 2019; mentioned approximately in US 116 million adults are explicitly afflicted by chronic pain. Chronic pain is described as dysfunction in nerves that have been continuous during a long period (Mills, 2019). Treatments for chronic pain are different types of common analgesics that relieve the pain for short periods such as aspirin, ibuprofen, paracetamol, …

A Phylogenetic Analysis Of Mycoplasma Strains Circulating In Sheep Pneumonia In Thekars Region Of Turkey, Olcay Öztürkler, Sali̇h Otlu

Turkish Journal of Veterinary & Animal Sciences

This study aimed to investigate Mycoplasma species by cultural and molecular methods in 250 pneumonics and 30 healthy appearance sheep lungs brought from slaughterhouse and butcheries in the Kars region of Turkey. The phylogenetic positioning of the bacterial strains to be obtained in the present study was another remarkable outcome of the study. Mycoplasma isolation was achieved solely in 26 (10.4%) of 250 sheep lungs with pneumonia. Mycoplasma ovipneumoniae was found predominant species in 12 (46.15%) of samples and that was followed by Mycoplasma arginini in 4 (15.38%) of strains. Moreover, two samples were found to be co-infected with the …

Environmental Dna Reveals Seasonal Shifts And Potential Interactions In A Marine Community, Anni Djurhuus, Collin J. Closek, Ryan P. Kelly, Kathleen J. Pitz, Reiko P. Michisaki, Hilary A. Starks, Kristine R. Walz, Elizabeth A. Andruszkiewicz, Emily Olesin, Katherine Hubbard, Enrique Montes, Daniel Otis, Frank E. Muller-Karger, Francisco P. Chavez, Alexandria B. Boehm, Mya Breitbart

Marine Science Faculty Publications

Environmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015–2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence …

Recolonization Potential For Coho Salmon (Oncorhynchus Kisutch) In Tributaries To The Klamath River After Dam Removal, Max M. Ramos

Cal Poly Humboldt theses and projects

Removal of four major dams on the Klamath River is scheduled to begin in 2023, restoring access to greater than 50 km of historic mainstem habitat for coho salmon. However, mainstem habitat may not be suitable for juvenile coho salmon due to elevated water temperatures and high concentrations of infectious myxospores in the summer and fast water velocities in the winter. Small, cooler tributaries can provide essential habitat for escape from deleterious conditions in the mainstem Klamath River. I used temperature and other physical features of six tributaries to the Klamath River above Iron Gate Dam to assess their capacity …

Alternative Water Sources In Western Conifers Via Foliar Uptake And Hydraulic Redistribution, Ariel Sol Weisgrau

Cal Poly Humboldt theses and projects

Water is often the most limiting resource in a plant’s environment. Plants that can maximize their ability to acquire water improve their chances of success. Outside of the traditional soil-plant-atmosphere continuum, plants can alternatively acquire water via foliar uptake of water and hydraulic redistribution (HR) of deep water. This study used greenhouse-based experiments to investigate water use and physiology in four conifer species native to the western U.S.: Picea sitchensis (Bong.) Carriére (PISI), Pseudotsuga menziesii (Mirb.) Franco (PSME), Sequoia sempervirens (D. Don) Endl. (SESE), and Thuja plicata Donn ex. D. Don (THPL). First, this work investigated the capacity for foliar …

Stimulated Growth Response To Sand Burial Of A Coastal Shrub, D. Nicole Keller

Theses and Dissertations

Drivers of vegetation zonation on barrier islands are complex and interconnected. Sand burial is a strong driver in dynamic coastal systems, especially in the foredune community. However, it is not well understood how burial impacts the interdunal swales communities and it is especially difficult to separate the effects of burial from salinity. Climate change is altering the frequency of overwash events as well as expanding the range of the native shrub, Morella cerifera, on the Virginia barrier islands. To accurately forecast island response to climate change it is important to understand how the shrub responds to sand burial. Juvenile …

The Influence Of Flooding On Macroinvertebrate Diversity Of The James River Rock Pools, Meghan Leber

Honors Theses

Biodiversity within an ecosystem can be greatly influenced by environmental disturbances, such as fires, flooding, or other extreme events. Studying the effects of these disturbances on species diversity can be complicated though, due to difficulties tracking species-level responses and isolating the effects of disturbances. Model systems in community ecology, such as rock pools, are a beneficial way to scale down the study of disturbances in discrete communities without losing the ability to analyze important influences or interactions. In this study, macroinvertebrates within the James River rock pools were surveyed to investigate seasonal and annual differences in species richness and diversity, …

Ailing In Place: Environmental Inequities And Health Disparities In Appalachia, Michele Morrone

Ohio University Press Open Access Books

In Ailing in Place, Michele Morrone explores the relationship between environmental conditions in Appalachia and health outcomes that are too often ascribed to individual choices only. She applies quantitative data to observations from environmental health professionals to frame the ways in which the environment, as a social determinant of health, leads to health disparities in Appalachian communities. These examples—these stories of place—trace the impacts of water quality, waste disposal, and natural resource extraction on the health and quality of life of Appalachian people.

Public health is inextricably linked to place. Environmental conditions such as contaminated water, unsafe food, and polluted …

Developing An Odonate-Based Index For Monitoring Freshwater Ecosystems In Rwanda: Towards Linking Policy To Practice Through Integrated And Adaptive Management, Erasme Uyizeye

Antioch University Dissertations & Theses

Worldwide, the decline of biodiversity in freshwater ecosystems is occurring at an alarming rate, due to anthropogenic threats, which directly impact humans in a variety of ways. Freshwater ecosystems occupy an integral part of political, socio-economic and ecological spheres. Integrated Watershed Management (IWM) and Adaptive Management (AM) conceptual frameworks provide an underpinning holistic platform from which to evaluate the performance of policies and actions on the ground in relation to freshwater ecosystem management. I investigate the extent to which environmental policies and practices embrace IWM and AM frameworks in Rwanda. Furthermore, this dissertation develops an odonate-based ecological monitoring tool, referred …

Plant Science Decadal Vision 2020–2030: Reimagining The Potential Of Plants For A Healthy And Sustainable Future, Natalie Henkhaus, Madelaine Bartlett, David Gang, Lonnie J. Guralnick, Et Al.

Arts & Sciences Faculty Publications

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 …

Cocktail Menus Ireland (1970s-2020) Version 1, James Murphy

Other resources

Cocktail Menus Ireland (1970s-2020) Version 1 highlights a small selection of cocktail menus from cocktail bars, public bars, hotel bars and Cocktail Clubs covering the period of 1970 up to 2020. These menus and their recipes help to identify the creativity, innovation and attention to detail in which the establishments highlighted here and their staff (cocktail bartenders, mixologists and management teams) poured into these menus. The menus also highlight the changing drinks fashions, how cocktail prices began to change, the variety of ingredients, the rise of the crafted approach towards ingredients sourcing and preparation. The impact of visual graphic illustrations, …

Coral Reefs In The Gulf Of Mexico Large Marine Ecosystem: Conservation Status, Challenges, And Opportunities, Diego L. Gil-Agudelo, Carlos E. Cintra-Buenrostro, Jorge Brenner, Patricia Gonzalez-Diaz, William Kiene, Caitlin Lustic, Horacio Perez-Espana

School of Earth, Environmental, & Marine Sciences Faculty Publications

The importance of coral reefs (CR) within marine ecosystems has become widely recognized. Although shallow CR are not as abundant in the Gulf of Mexico (GoM) as in other areas such as the Caribbean, their uniqueness, singularity, isolation, and conservation status make their conservation highly important. Corals and CR, both shallow and deep, are more widely distributed throughout the GoM than previously thought, providing new venues of research but also new challenges for their sustainable management. They are widely present in the three countries circumscribing the GoM (Cuba, Mexico, and the United States). Corals are also distributed throughout different depths, …

Genetic Variation Within A Broadly Distributed Chewing Louse Genus (Thomomydoecus), Clarissa Elizabeth Bruns

Honors Program Theses

No broad study has been conducted to examine the genetics of Thomomydoecus species and their patterns of geographic variation. Chewing lice and their parasite-host relationships with pocket gophers have been studied as a key example of cophylogeny (Demastes et al., 2012). Despite this, genetic data on interspecific and intraspecific variation in Thomomydoecus is unexplored, and prior studies consisted within the narrow frame of one complex or species and its relative host gopher. This project collected, and analyzed genetic data, then generated phylogenetic trees. Many of the existing relationships between Thomomydoecus species was confirmed, and there were a number of unexpected …

The Role Of Topography, Soil, And Remotely Sensed Vegetation Condition Towards Predicting Crop Yield, Trenton E. Franz, Sayli Pokal, Justin P. Gibson, Yuzhen Zhou, Hamed Gholizadeh, Fatima Amor Tenorio, Daran Rudnick, Derek M. Heeren, Matthew F. Mccabe, Matteo Ziliani, Zhenong Jin, Kaiyu Guan, Ming Pan, John Gates, Brian Wardlow

School of Natural Resources: Faculty Publications

Foreknowledge of the spatiotemporal drivers of crop yield would provide a valuable source of information to optimize on-farm inputs and maximize profitability. In recent years, an abundance of spatial data providing information on soils, topography, and vegetation condition have become available from both proximal and remote sensing platforms. Given the wide range of data costs (between USD $0−50/ha), it is important to understand where often limited financial resources should be directed to optimize field production. Two key questions arise. First, will these data actually aid in better fine-resolution yield prediction to help optimize crop management and farm economics? Second, what …

Comments On The Preliminary Framework For Equitable Allocation Of Covid-19 Vaccine, Ana Santos Rutschman, Julia Barnes-Weise, Robert Gatter, Timothy L. Wiemken

All Faculty Scholarship

On September 1, 2020 the National Academies released a draft framework for Equitable Allocation of a COVID-19 Vaccine. In this response, we analyze the proposed framework and highlight several areas.

Among the proposed changes, we highlight the need for the following interventions. The final framework for distribution of COVID-19 vaccines should give a higher priority to populations made most vulnerable by the social determinants of health. It should incorporate more geography-based approaches in at least some of the four proposed phases of vaccine distribution. It should address the possibility of a vaccine being made available through an emergency use authorization …

Biosecurity Levels Of Livestock Enterprises In Turkey And Factors Affecting These Levels, Mehmet Feri̇t Can, Nuri̇ Altuğ, Ferhan Kaygisiz

Turkish Journal of Veterinary & Animal Sciences

Biosecurity (BS) is a multidimensional preventive medicine approach that has health, technical, and financial aspects. The purpose of this study was to determine the differences of the BS scores belonging to the livestock enterprises depending on the geographical region and breeding types and to predict the socioeconomic factors having an impact over the BS level. The study was conducted with 517 breeders who live in 7 different regions of Turkey. The results have revealed that the enterprises performing "beef cattle fattening and dairy cattle breeding together" have higher BS scores than the enterprises in the other breeding category (P < 0.01). The differences between the technical and financial scores according to geographical regions were statistically significant (P < 0.01). The regions categorized as "wes" have the highest score and "south" have the lowest score. It was determined that as the "educational level of the breeder" and "enterprise scale" increased, the BS score significantly went up. The regression model was found significant as a whole (P < 0.01) and the independent variables explained the variation in the technical and financial BS scores to be 14.6% and 12.7%, respectively. Dissemination of education/training practices and increasing enterprise scales will positively affect the level of BS in the sector.

Estimating Evolutionary Volatility In A Maximum-Likelihood Framework, Samuel Warren Tybout

Graduate Theses, Dissertations, and Problem Reports (ETD)

Evolutionary volatility is a trait that encompasses a clade’s combined capacity for origination and extinction. High volatility increases extinction risk, and declining global extinction rates are thought to be linked to declining volatility. Despite volatility’s scientific importance, there is no standardized way of measuring it. This study provides a new method, derived from a stochastic birth-death model, of estimating evolutionary volatility from fossil data. Simulations indicate that the method produces accurate and precise estimates for large fossil datasets. Analysis of fossil data for five bivalve families (Lucinidae, Mytilidae, Pectinidae, Pholadomyidae, and Veneridae) indicates that diversity projections made from the estimates …

An Alien Species Or Another Perspective To The Freshwater Gobies Puzzle: A New Finding Inlake Prespa, Blagoja Trajchevski, Zoran Spirkovski, Dushica Ilikj-Boeva, Trajce Talevski

Turkish Journal of Zoology

Here we present a discovery of a new fish from the family Gobiidae in Lake Prespa, which is known as a European hotspot for biodiversity and endemism. This is the first detection of a fish species from this family, not only regarding this lake but also in the territory of the Republic of North Macedonia in general. The close examination of the recorded specimens revealed the presence of perianal organ surrounding the anus. This unique organ and various other observed morphometric and phenotypic characteristics point out to the genus Economidichthys. The two known fish species from this genus are currently …

A Justification For Continued Management Of Turfgrass During Economic Contraction, James T. Brosnan, Ambika Chandra, Roch E. Gaussoin, Alec Kowalewski, Bernd Leinauer, Frank S. Rossi, Douglas J. Soldat, John C. Stier, J. Bryan Unruh

Department of Agronomy and Horticulture: Faculty Publications

A novel coronavirus, termed COVID-19, spread worldwide and become a global pandemic in 2020. Forecasts show that COVID-19 will cause substantial economic contraction affecting almost every industry. Managed turfgrass, particularly in urban settings, has many positive societal and environmental benefits. In a contracted economy, will resources be available to manage turfgrass to achieve these benefits? In this paper, we outline the benefits of managed turfgrass on golf courses, playing fields, recreational parks, and urban landscapes to assist decision makers with resource allocation in the COVID-19 era.