Digital Commons Network^™

Modeling Chlorophyll Concentrations On The Ohio River Using Remotely Sensed Data, Thaddaeus Stephen Tuggle

Theses, Dissertations and Capstones

Traditional direct water quality methodologies limit the ability to spatially and temporally predict algal blooms in lotic systems due to the size and characteristics of large river systems. Algal blooms potentially can be predicted by knowing the spatial and temporal patterns of change in cyanobacteria concentrations at large scales. Remote sensing studies investigating freshwater algal blooms, some known to secrete harmful toxins, are primarily conducted on lentic systems while large lotic systems are greatly ignored. In this study I developed a chlorophyll concentration estimation model for the Ohio River using a satellite remote sensing approach. Ground-truth water quality measures, including …

Using Environmental Dna And Occupancy Modeling To Examine Drivers Of Eastern Hellbender Extirpation And Sampling Method Efficiency In West Virginia, Sean Michael Wineland

Theses, Dissertations and Capstones

Amphibian population declines and range constrictions are widespread but poorly understood. Effective conservation planning relies on accurate distribution data to develop a fundamental understanding of causal changes in species distributions. However, conventional detection methods for cryptic and elusive amphibians suffer from imperfect detection. Environmental DNA (eDNA) has emerged as an innovative and powerful conservation tool for detecting aquatic species presence; however comparative studies aimed at fully understanding eDNA detection probabilities are lacking. In this study, I used environmental DNA (eDNA) sampling methods and detailed historical records to identify drivers of extirpation and sampling method efficiency for an imperiled, long-lived giant …

Southern Fox Squirrel (Sciurus Niger Niger) Translocation, Occupancy, And Foraging Behaviors, Katelyn Marie Amspacher

Theses, Dissertations and Capstones

Southern fox squirrels (SFSs) are habitat specialists within the longleaf pine ecosystem of the southeastern US whose populations are declining due to habitat fragmentation. Eastern gray squirrels (EGSs) are generalists found throughout the eastern US that have historically avoided competition with SFSs through habitat-partitioning. The purpose of this study was threefold: 1) use translocation as a conservation tool to establish a population of SFSs on Marine Corps Recruit Depot Parris Island (MCRDPI), South Carolina and monitor survival, home range size, and habitat use post-translocation, 2) estimate SFS density on Spring Island, SC and examine patterns of SFS and EGS occupancy, …

A Characterization Of West Virginia Coyotes (Canis Latrans) Utilizing Skull Morphology, Katharina E. Scholer

Theses, Dissertations and Capstones

Coyotes (Canis latrans) are now found throughout North and Central America, but before European colonization were restricted to west of the Mississippi. Migration occurred in two major paths to the East; north over the Great Lakes (through Canada) and south below the Great Lakes. The location of these routes is significant because those migrating north interbred with the wolves that reside there. These hybrid animals are larger and behaviorally different from their western counterparts. It is possible to differentiate these hybrids morphologically and genetically. Hybrids are known to be located in Maine, New York, and Pennsylvania, but the interest of …

Freshwater Mussels Of The Greenup Navigational Pool, Ohio River, With A Comparison To Fish Host Communities, Mitchell David Kriege

Theses, Dissertations and Capstones

The Ohio River was historically a free-flowing system with diverse fish and freshwater mussel communities. Heavy industrialization, erosion from deforestation, and wide scale damming during the early-mid 20th century decimated riverine life. While mussel declines are well documented in the United States, in big river systems, freshwater mussel populations are poorly understudied. This thesis project mapped the mussel communities and site-specific sediments of the Greenup pool in the Ohio River for comparison to 2016 nighttime electrofishing data, provided by ORSANCO. Qualitative SCUBA surveys were performed at 18 randomly selected sites and two fixed sites between July and September. Each site …

Amphibians Among Road-Rut Pools In West Virginia, Abby L. Sinclair

Theses, Dissertations and Capstones

As anthropogenic environmental stressors such as urbanization continue to increase, it is necessary to understand their impact on amphibian ecology. Due largely to their biphasic life history amphibians are negatively impacted by the destruction of lotic habitats i.e., wetlands for the creation of roads and urban centers. I examined the effects of three human-made road rut pools on the reproductive success and species richness of amphibians in southwest West Virginia from May to October 2012. I employed three detection techniques: drift fence pitfall trap arrays, funnel traps and dipnet sampling. Additionally, habitat covariates were taken (i.e., water depth) at each …

Influence Of Developmental Stage, Habitat, And Captivity On Thecutaneous Bacterial Communities Of Eastern Hellbenders (Cryptobranchus Alleganiensis Alleganiensis) In West Virginia, Rachel Fern Arrick

Theses, Dissertations and Capstones

Microbes inhabit virtually all surfaces of multicellular animal hosts, with microbial cells outnumbering the hosts’ own cells 10:1. Symbiont microbes, collectively referred to as the microbiome, can have profound impacts on the metabolism, development, behavior, and disease resistance of their multicellular hosts. Because the community structure of symbiont bacteria can influence host health, the characterization of amphibian microbiomes is becoming an increasingly important tool for future conservation in the face of global amphibian declines. Eastern hellbenders are good candidates for a microbiome study because they have seen substantial declines in recent decades and learning more about the environmental and physiological …

Audiobook Of A World From Dust, Ben Mcfarland

Faculty Open Access Books

A World From Dust is a popular science book about the chemical sequence behind the evolution of creation.

It’s about how geology, biology, and chemistry worked together over billions of years, providing a hidden order under the random flow of genes and lava and water.

It’s about the chemical job that each element takes up in life, and how that job is predictable from its place on the periodic table.

It can be told as the story of many elements: how iron and sulfur gave a spark of life; how manganese was a key for oxygen; and how copper and …

Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes b3725, b3726, b3727, b3728 and Mrub_2518, Mrub_2519, Mrub_2520 and Mrub_2521 (KEGG map number 02010). We predict that these genes encode the components of a Phosphate ABC transporter: Orthologous genes Mrub_2518 (DNA coordinates 2565359..2566438) and b3728 encodes the periplasmic phosphate binding component; Orthologous genes Mrub_2519 (DNA coordinates 2566499..2567485) and b3727, and Mrub_2520 (DNA coordinates 2567496..2568326) and b3726 encode for the two transmembrane proteins; Orthologous genes Mrub_2521 (DNA coordinates 2568338..2569159) and b3725 encode for the ATP binding protein within the cytoplasm. Within the two species, M. ruber and E. coli, …

Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 (KEGG map number 02010). We predict these genes encode components of a Branched Chain Amino Acid ATP Binding Cassette (ABC) transporter: 1) Mrub_1325 (DNA coordinates 1357399-1358130 on the reverse strand) encodes the ATP binding domain; 2) Mrub_1326 (DNA coordinates 1358127-1359899 on the reverse strand) encodes the ATP-binding domain and permease domain; 3) Mrub_1327 (DNA coordinates 1359899-1360930 on the reverse strand) encodes a permease domain; and 4)Mrub_1328 (DNA coordinates 1711022-1712185 on the reverse strand) encodes the substrate binding domain. This system is not predicted to …

Mrub_1283, Mrub_1284 And Mrub_1285 Encode For A Glycine/Betaine Abc Transporter And Are Orthologs Of E. Coli Prov, Prow And Prox, Lan Dang, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABC transporters are essential for cellular transport; contribute to maintain the homeostasis of the cells. Generally, ABC transporters are multi-subunit; contain essential cytoplasmic factors which are critical to ATP hydrolysis activity. In this paper, we would like to take a closer look to Mrub_1283, Mrub_1284 and Mrub_1285, three consecutive genes in Meiothermus ruber genome. We hypothesize that these genes are in the same operon and encode for ABC glycine/ betaine transporters. To confirm our hypothesis, we utilizes several bioinformatics tools to predict the potential function of Mrub_1283, Mrub_1284 and Mrub_1285 and to search for their orthologs in Escherichia coli genome. …

Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 And Mrub_2124 Are Orthologs Of E. Coli Genes B3458, B3457, B3456, B3455 And B3454, Respectively, And Make Up An Operon That Codes For The Branched-Chain Amino Acid Abc Transporter In Meiothermus Ruber Dsm 1279, Aaron Jones, Madelyn Huber, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 and Mrub_2124 (KEGG map number 02010). We predict these genes encode components of a branched-chain amino acid ATP Binding Cassette (ABC) transporter: 1) Mrub_2120 (DNA coordinates 2169247-2170416 on the reverse strand) encodes the branched-chain amino acid binding protein that is localized to the periplasm; 2) Mrub_2121 (DNA coordinates 2170433..2171353 on the reverse strand) encodes the first TMD; 3) Mrub_2122 (DNA coordinates 2171365..2172279 on the reverse strand) encodes the second TMD; 4) Mrub_2123 (DNA coordinates 2172276..2173028 on the reverse strand) encodes the first NBD; 5) Mrub_2124 …

Mrub_1675, Mrub_1676, Mrub_1677, And Mrub_1679 Genes Are Orthologs Of B_3458, B_3457, B_3456, And B_3454 Genes In E. Coli, Respectively, Coding For Abc Transporters. Mrub_1678 And B_3455, Though Perform Similar Tasks, Are Not Orthologous, Ravi Patel, Alaina Hofmann, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1675, Mrub_1676, Mrub_1677, and Mrub_1679 (KEGG map number 02010). We predict these genes encode components of a Branched chain amino acid (ABC) transporter: Mrub_1675 (DNA coordinates 1711022..1712185 on the reverse strand) encodes the permease component, Mrub_1676 (DNA coordinates 1712313..1713170) encodes for the NBD (aka nucleotide binding domain), Mrub_1677 (DNA coordinates 1713167..1714075 on the reverse strand) encodes the NBD (aka nucleotide binding domain), Mrub_1678 (DNA coordinates 1713167..1714075 on the reverse strand) encodes the TMD (aka transmembrane domain) and Mrub_1679 (DNA coordinates 1714781..1715485 on the reverse strand) encodes …

Mrub_0680, Mrub_0836, And Mrub_0837 Found To Be Orthologous To E. Coli Ccma, Ccmb, And Ccmc, Respectively, Coding For Abc-Transport Proteins Involved In Cytochrome-C Biogenesis, Sarah N. Church, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_0680, Mrub_0836 and Mrub_0837(KEGG map number 02010). We predict these genes encode components of a Heme ATP Binding Cassette (ABC) transporter: 1) Mrub_0836 (DNA coordinates 823734..824399on the reverse strand) encodes the permease component (aka transmembrane domain), predicted to be an ortho; and 2) Mrub_0680(DNA coordinates 659484..660071 on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_0837(DNA coordinates 824570..825262on the reverse strand) encodes the solute binding protein. This gene system encodes a transmembrane exporter and helper proteins which are thought to …

Meiothermus Ruber Mrub_0320 Gene Is An Ortholog Of The B3452 Gene, Mrub_0321 Gene Is An Ortholog Of The B3451 Gene, Mrub_0322 Gene Is An Ortholog Of The B3453 Gene, Mrub_2366 Gene Is An Ortholog Of The B3450 Gene Found In Escherichia Coli, Which Encode For Components Of An Abc Transporter Involved In Sn-Glycerol - 3-Phosphate, Jenna Hall, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes mrub_0320, mrub_0321, mrub_0322, and mrub_2366 (KEGG map number 02010). We predict these genes encode components of a sn-glycerol-3-phosphate (ABC) transporter: 1) mrub_0320 (DNA coordinates 288469..289401) encodes the permease component (aka transmembrane domain), predicted to be an ortholog; 2) mrub_0321 (DNA coordinates 289394..290218) encodes another permease domain, and also contains a transcriptional regular; ATP-binding domain (aka nucleotide binding domain); 3) mrub_0322 (DNA coordinates 290234..291541) encodes the solute binding protein; and 4) mrub_2366 (DNA coordinates 2418207..2419352 on the reverse strand) encodes for an ATP-binding domain for multiple sugar-related ABC transport systems …

Responses Of Early-Successional Songbirds To A Two-Stage Shelterwood Harvest For Oak Forest Regeneration, Eric L. Margenau, Yong Wang, Callie J. Schweitzer

Faculty & Staff Scholarship

Background: The early stage of forest succession following disturbance is characterized by a shift in songbird com- position as well as increased avian richness due to increased herbaceous growth in the forest understory. However, regeneration of woody species eventually outcompetes the herbaceous understory, subsequently shifting vegetation communities and decreasing availability of vital foraging and nesting cover for disturbance-dependent birds, ulti- mately resulting in their displacement. These early stages following forest disturbance, which are declining through- out the eastern United States, are ephemeral in nature and birds depend on such disturbances for nesting and other purposes throughout their lives.

Methods: We …

Modular Structure In Fish Co-Occurrence Networks: A Comparison Across Spatial Scales And Grouping Methodologies, Daniel Mcgarvey Dr., Joseph Veech

Environmental Studies Publications

Network modules are used for diverse purposes, ranging from delineation of biogeographical provinces to the study of biotic interactions. We assess spatial scaling effects on modular structure, using a multi-step process to compare fish co-occurrence networks at three nested scales. We first detect modules with simulated annealing and use spatial clustering tests (interspecific distances among species’ range centroids) to determine if modules consist of species with broadly overlapping ranges; strong spatial clustering may reflect environmental filtering, while absence of spatial clustering may reflect positive interspecific relationships (commensalism or mutualism). We then use non-hierarchical, multivariate cluster analysis as an alternative method …

Diet Breadth Evolution And Diversification Of A Generalist Insect Herbivore, Mayra Cadorin Vidal

Electronic Theses and Dissertations

Insect herbivores are one of the most diverse groups of multicellular organisms, and the vast majority are specialists, which feed on only a few plant species. The factors that cause some herbivores to be specialists and others to be generalists are still unclear. It is known that the selective forces from natural enemies (top-down) and the host plants (bottom-up) influence an herbivore's diet breadth. In my meta-analysis evaluating the relative important of top-down and bottom-up forces on insect herbivore fitness, I found that herbivores usually have greater performance on better quality plants and in the absence or reduction of enemy …

Social Conflict On The Seas: Links Between Overfishing-Induced Marine Fish Stock Declines And Forced Labor Slavery, Jessica L. Sparks

Electronic Theses and Dissertations

Despite media attention detailing labor abuses in fisheries, social-ecological systems research has largely failed to consider whether fish stock declines could be contributing to increases in forced labor slavery. Empirical fisheries data suggests, though not a ubiquitous response to declining stocks, many vessels will fish longer, farther from shore, and deeper in waters to maintain yields. This effort intensification increases production costs, and Brashares et al. (2014), consistent with slavery theory, posited cheap and/or unpaid labor as an approach to offset increasing costs and continue harvesting fish species at a rate otherwise cost-prohibitive.

Using fuzzy cognitive mapping - a participatory, …

Effects Of Anthropogenic Noise On Mating Behavior And Fitness, Gabrielle A. Gurule-Small

Electronic Theses and Dissertations

When environments change rapidly, adaptive phenotypic plasticity can ameliorate negative effects of environmental change on survival and reproduction. Recent evidence, however, suggests that plastic responses to human induced environmental change are often maladaptive or insufficient to overcome novel selection pressures. Anthropogenic noise is a ubiquitous and expanding disturbance with demonstrated effects on fitness-related traits of animals like stress responses, foraging, vigilance, and pairing success. Elucidating the lifetime fitness effects of noise has been challenging because long-lived vertebrate systems are typically studied in this context. In both chapters described herein, I reared field crickets, Teleogryllus oceanicus, in masking traffic noise, …

Examination Of Enrichment Using Space And Food For African Elephants At The Sdzsp, Charlotte Hacker, Lance Miller, Bruce A. Schulte

Biology Faculty Publications

Concern for elephant welfare in zoological facilities has prompted a number of exhibit and management modifications, including those involving enrichment. Knowledge of how these changes impact indicators of welfare, such as elephant movement and behaviour, is crucial for continued improvement of elephant husbandry and care. The present study used observations and GPS-collected data to determine the effects of available space and food presentation on the walking distance and behaviour of thirteen African elephants (Loxodonta africana), which had a dominance structure ascertained by animal care staff at the San Diego Zoo Safari Park (SDZSP). This facility has two exhibits of approximately …

The Political Biogeography Of Migratory Marine Predators, Autumn-Lynn Harrison, Daniel Costa, Arliss Winship, Scott Benson, Steven Bograd, Michelle Antolos, Aaron Carlisle, Heidi Dewar, Peter Dutton, Salvador Jorgensen, Suzanne Kohin, Bruce Mate, Patrick Robinson, Kurt Schaefer, Scott A. Shaffer, George Shillinger, Samantha Simmons, Kevin Weng, Kristina Gjerde, Barbara Block

Faculty Publications, Biological Sciences

During their migrations, marine predators experience varying levels of protection and face many threats as they travel through multiple countries’ jurisdictions and across ocean basins. Some populations are declining rapidly. Contributing to such declines is a failure of some international agreements to ensure effective cooperation by the stakeholders responsible for managing species throughout their ranges, including in the high seas, a global commons. Here we use biologging data from marine predators to provide quantitative measures with great potential to inform local, national and international management efforts in the Pacific Ocean. We synthesized a large tracking data set to show how …

Environmental Effects On Drosophila Brain Development And Learning, Xia Wang, Amei Amei, J. Steven De Belle, Stephen P. Roberts

Biological Sciences Faculty Research & Creative Works

Brain development and behavior are sensitive to a variety of environmental influences including social interactions and physicochemical stressors. Sensory input in situ is a mosaic of both enrichment and stress, yet little is known about how multiple environmental factors interact to affect brain anatomical structures, circuits and cognitive function. In this study, we addressed these issues by testing the individual and combined effects of sub-adult thermal stress, larval density and early-adult living spatial enrichment on brain anatomy and olfactory associative learning in adult Drosophila melanogaster. In response to heat stress, the mushroom bodies (MBs) were the most volumetrically impaired among …

The Roles Of Inter- And Intra-Sexual Selection In Behavioral Isolation Between Native And Invasive Pupfishes, Cory Becher, Jennifer M. Gumm

Faculty Publications

Male-male competition and female mate choice may both play important roles in driving and maintaining reproductive isolation between species. When previously allopatric species come into secondary contact with each other due to introductions, they provide an opportunity to evaluate the identity and strength of reproductive isolating mechanisms. If reproductive isolation is not maintained, hybridization may occur. We examined how reproductive isolating mechanisms mediate hybridization between endemic populations of the Red River pupfish Cyprinodon rubrofluviatilis and the recently introduced sheepshead minnow C. variegatus. In lab-based dominance trials, males of both species won the same number of competitions. However, male C. rubrofluviatilis …

Origins Of Animal Cell Adhesion, Jennyfer Mora Mitchell

Electronic Theses and Dissertations

A fundamental requirement for multicellularity is cell adhesion. This includes mechanisms by which cells adhere to each other and to their secreted extracellular matrix (ECM). Two well characterized adhesion complexes in animals include: 1) adherens junctions (AJs), which are involved in cell-cell adhesion and composed of cadherin receptors, p120-, α- and β-catenin, and 2) focal adhesions (FAs), which are involved in cell-ECM adhesion and include proteins such as integrins, vinculin, paxillin, talin and focal adhesion kinase (FAK). The molecular components of AJs are widely conserved in animals, and largely absent in non-animals. In contrast, the molecular components of FAs have …

Sequestered Alkaloid Defenses In The Dendrobatid Poison Frog Oophaga Pumilio Provide Variable Protection From Microbial Pathogens, K. J. Hovey, E. M. Seiter, Erin E. Johnson, Ralph Saporito

2018 Faculty Bibliography

Most amphibians produce their own defensive chemicals; however, poison frogs sequester their alkaloid-based defenses from dietary arthropods. Alkaloids function as a defense against predators, and certain types appear to inhibit microbial growth. Alkaloid defenses vary considerably among populations of poison frogs, reflecting geographic differences in availability of dietary arthropods. Consequently, environmentally driven differences in frog defenses may have significant implications regarding their protection against pathogens. While natural alkaloid mixtures in dendrobatid poison frogs have recently been shown to inhibit growth of non-pathogenic microbes, no studies have examined the effectiveness of alkaloids against microbes that infect these frogs. Herein, we examined …

Male Mate Preference As An Agent Of Fecundity Selection In A Polymorphic Salamander, Kortney E. Jaworski, Matthew S. Lattanzio, Cari-Ann M. Hickerson, Carl D. Anthony

2018 Faculty Bibliography

Color polymorphisms are associated with variation in other traits which may affect individual fitness, and these color‐trait associations are expected to contribute to nonrandom mating in polymorphic species. The red‐backed salamander (Plethodon cinereus) exhibits a polymorphism in dorsal pattern: striped and unstriped, and previous studies have suggested that they may mate nonrandomly. However, the mechanism(s) contributing to this behavior remain unclear. Here we consider the role that male preference may have in driving mating behavior in P. cinereus. We limit our focus to striped individuals because this morph is most likely to be choosy given their dominant, aggressive behavioral profiles …

Chickens Play To The Crowd, Cinzia Chiandetti

Animal Sentience

The time was ripe for Marino’s review of chickens’ cognitive capacities. The research community, apart from expressing gratitude for Marino’s work, should now use it to increase public awareness of chickens’ abilities. People’s views on many animals are ill-informed. Scientists need to communicate and engage with the public about the relevance and societal implications of their findings.

Post-Darwin Skepticism And Run-Of-The-Mill Suicide, John Hadley

Animal Sentience

Peña-Guzmán’s depiction of the opponent of animal suicide as a conservative is a straw man. It is possible to accept that animals are self-conscious and reflexive yet still reject the view that they have the mental wherewithal to commit run-of-the-mill suicide. That animal behaviour can be positioned on a continuum of self-destructive behaviour does not establish that animals can intentionally kill themselves.

An Adaptationist Perspective On Animal Suicide, Timothy P. Racine

Animal Sentience

Peña-Guzmán’s discussion of suicide in nonhuman animals has broad implications. In this commentary, I focus on the logical relation between suicide and intention. Proximate cause must be distinguished from ultimate function in explanations of suicide. I briefly discuss two adaptationist accounts of suicidal behavior.