Ecology and Evolutionary Biology Commons^™

Are Mussel Shells Environmental Dna Time Capsules? A Comparison Of Extraction Methods For Obtaining Dna From Shell Material., Kelsey Elizabeth Rogers

Online Theses and Dissertations

Freshwater mussels have become some of the most imperiled species in North America and widespread populations have succumbed to pollution and many other anthropogenic-related factors. With molecular techniques evolving, a recent interest in ancient DNA and museum specimens has emerged and prompted a study to test the ability of several extraction methods to isolate DNA from museum mussel specimens. The purpose of this study was to determine if four DNA extraction methods had influence on total DNA yield (ng/mg) from mussel tissue. The hinge ligaments of freshwater mussels ranging in collection date (1984-2015) were used as the source of genetic …

Natural Environmental Gradients Predict The Microhabitat Use, Fine-Scale Distribution, And Abundance Of Three Woodland Salamanders In An Old-Growth Forest, Joseph Alex Baecher

Online Theses and Dissertations

Woodland salamanders (Plethodonidae: Plethodon)－a group of sensitive, direct developing, lungless amphibians－are particularly responsive to gradients in environmental conditions. Because of their functional dominance in terrestrial ecosystems, woodland salamanders are responsible for the transformation of nutrients and translocation of energy between highly desperate levels of trophic organization (detrital food webs and high‐order predators). However, the spatial extent of woodland salamanders' role in the ecosystem is likely contingent upon the distribution of their biomass throughout the forest. Therefore, a better understanding of woodland salamander spatial population dynamics is needed to further understand their role in terrestrial ecosystems. The objectives of this study …

Comparison Of Cytochrome B Variation And Morphological Features Of Isolated Banded Pygmy Sunfish (Elassoma Zonatum) Populations In The Lower Green River And Coastal Plain Systems In Western Kentucky, David Cravens

Online Theses and Dissertations

The banded pygmy sunfish Elassoma zonatum is a wide-ranging species found throughout the Southeastern Coastal Plain of North America. In Kentucky, the populations are found above and below the inner boundary of the Coastal Plain. Due to their geographical separation comparisons in body size and morphological features along with genetic comparisons using mitochondrial cytochrome-b (Cyt-b) were conducted to test relationships between populations. Two sites, Cypress Creek in the Lower Green River system and Rose Creek in the Tradewater River drainage, were sampled from above the inner boundary and two additional sites, Bayou de Chien and Running Slough in the Mississippi …

Sample Collection And Dna Extraction Methods For Environmental Dna Metabarcoding In Headwater Streams, Michael Triston Mullins

Online Theses and Dissertations

DNA is found to be free and ubiquitous in the environment where it is no longer associated with the source organism, and is also known as environmental-DNA (eDNA). Methods optimized for specific environments may be able supplement insight to local taxa richness. With the advent of high throughput sequencing and the proliferation of sequence data in public repositories, insights to the biodiversity of communities at the molecular level have been possible. Thus, this study compared commonly used DNA capture (water precipitation and filtration) and extraction (MoBio's PowerWater, Qiagen's DNeasy Blood and Tissue Kit, and a CTAB protocol) methods in their …

Assessment Of The Macroinvertebrate Assemblages From The Mesohabitats Of A Headwater Stream-Wetland Hydrologic Restoration In Eastern Kentucky, Rebecca Jo Roberts

Online Theses and Dissertations

The bulk of streams in the U.S. have been negatively impacted by anthropogenic disturbances and the streams of Kentucky are no exception. In recent decades stream restoration has become a common practice in order to improve habitat degradation resulting from land use practices such as channelization. Despite the large amount of effort and funding stream restoration projects represent, only a small portion have undergone post-restoration assessments of the ecological response in the restored streams. Slabcamp Creek, a headwater stream located in the Licking River basin in eastern Kentucky, underwent a stream-wetland hydrologic restoration in 2010 in order to improve hydrologic …

Glucocorticoids And Parental Effort In Tree Swallows (Tachycineta Bicolor), Mackenzie Prichard

Undergraduate Theses, Professional Papers, and Capstone Artifacts

All vertebrates respond to stressful situations through the release of hormones called glucocorticoids (CORT). These hormones alter processes within the body to prioritize long term survival over immediate reproduction. It is hypothesized that this is helps individuals survive until conditions become more favorable for successful reproduction. Historically, stress was hypothesized to primarily to pull organisms out of reproductive life history stages when unfavorable conditions made offspring survival slim (otherwise known as the “CORT-tradeoff hypothesis”). However, recent evidence suggests that birds actively feeding nestlings show elevated CORT levels, possibly due to the increased metabolic demands of parenthood. This relationship has been …

Toward Estimating Displaced Primary Production From Recycling: A Case Study Of U.S. Aluminum, Trevor Zink

Management Faculty Works

Recycling materials from end-of-life products has the potential to create environmental benefit by displacing more harmful primary material production. However, displacement is governed by market forces and is not guaranteed; if full displacement does not occur, the environmental benefits of recycling are reduced or eliminated. Therefore, quantifying the true “displacement rate” caused by recycling is essential to accurately assess environmental benefits and make optimal environmental management decisions. Our 2016 article proposed a market-based methodology to estimate actual displacement rates following an increase in recycling or reuse. The current article demonstrates the operation, utility, and challenges of that methodology in the …

Invasion Dynamics Of The Exotic Liana Euonymus Fortunei (Turcz.) Hand.-Mazz. (Wintercreeper), Todd J. Rounsaville

Theses and Dissertations--Biology

Elevated atmospheric CO₂ has been implicated as a driver of increased liana abundance worldwide. Known as disturbance creators and beneficiaries, lianas possess the potential to significantly influence forest ecosystems. I investigated the early-invasion dynamics of Euonymus fortunei (wintercreeper), an evergreen liana that is invading forests in eastern North America, disrupting native plant communities and ecosystem functions.

Wintercreeper is widely cultivated as an ornamental groundcover, frequently invading natural areas via asexual stem growth. Invasion of remote natural areas is dependent upon seed transport and may occur less frequently. I examined the mechanisms of seed dormancy by conducting a ‘move-along’ experiment …

Genetic Perspectives On Biodiversity In Rocky Mountain Alpine Streams, Scott Hotaling

Theses and Dissertations--Biology

In alpine regions worldwide, climate change is dramatically altering ecosystems, affecting biodiversity across habitats and taxonomic scales. For streams, the associated recession of mountain glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, and basal resources – often threatening the very existence of some habitats and biota. Globally, alpine streams harbor particularly substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity: however, anthropogenic warming threatens to homogenize habitats through the reduction of the cryosphere, thereby reducing biodiversity from micro- to macroscopic organisms and genes to communities. Still, alpine stream biodiversity, …

Mitochondrial And Nuclear Patterns Of Conflict And Concordance At The Gene, Genome, And Behavioral Scales In Desmognathus Salamanders, Justin D. Kratovil

Theses and Dissertations--Biology

Advancements in molecular sequencing have revealed unexpected cryptic genetic diversity and contrasting evolutionary histories within genes and between genomes of many organisms; often in disagreement with recognized taxonomy. Incongruent patterns between the mitochondrial and nuclear evolutionary history can have several plausible explanations, but widespread systematic conflict inevitably challenges our conceptions of species boundaries when there is discordance between coevolving and coinherited genomes. It is unknown to what degree mitonuclear conflict drives the process of divergence, or how ubiquitous these patterns are across the tree of life. To understand the evolutionary relevance of intergenomic discordance we must identify the conflicting patterns …

Using Genomics To Understand Population Demographics In The Context Of Amphibian Conservation, Schyler O. Nunziata

Theses and Dissertations--Biology

Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Large single nucleotide polymorphism datasets generated with restriction-site associated DNA sequencing (RADseq), in combination with demographic inference methods, are improving our ability to gain insights into the population history of both model and non-model species. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography, in both simulation and empirical settings. Here, I used a simulation approach to examine the potential for RADseq datasets to accurately estimate effective population size (N_e) in Wright-Fisher populations over the course of stable and declining population trends, and distinguish stable from steadily declining populations over a contemporary time scale (20 generations). Overall, my results reveal that demographic inference using genome-wide data can be successfully applied to estimate N_e, and the detection of population-size declines. Next, I assess these methods in an empirical study from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and …

Genomic Perspectives On Amphibian Evolution Across Multiple Phylogenetic Scales, Paul Michael Hime

Theses and Dissertations--Biology

Genomes provide windows into the evolutionary histories of species. The recent accessibility of genome-scale data in non-model organisms and the proliferation of powerful statistical models are now providing unprecedented opportunities to uncover evolutionary relationships and to test hypotheses about the processes that generate and maintain biodiversity. This dissertation work reveals shallow-scale species boundaries and population genetic structure in two imperiled groups of salamanders and demonstrates that the number and information content of genomic regions used in species delimitation exert strong effects on the resulting inferences. Genome scans are employed to test hypotheses about the mechanisms of genetic sex determination in …

Evaluation Of Smartstax And Smartstax Pro Maize Against Western Corn Rootworm And Northern Corn Rootworm: Efficacy And Resistance Management, Graham P. Head, Matthew W. Carroll, Sean P. Evans, Dwain M. Rule, Alan R. Willse, Thomas L. Clark, Nicholas P. Storer, Ronald D. Flannagan, Luke W. Samuel, Lance Meinke

Department of Entomology: Faculty Publications

Background: Cases of western corn rootworm (WCR) field-evolved resistance to Cry3Bb1 and other corn rootworm (CRW) control traits have been reported. Pyramid products expressing multiple CRW traits can delay resistance compared to single trait products. We used field studies to assess the pyramid CRW corn products, SmartStax (expressing Cry3Bb1 and Cry34Ab1/Cry35Ab1) and SmartStax PRO (expressing Cry3Bb1, Cry34Ab1/Cry35Ab1 and DvSnf7), at locations with high WCR densities and possible Cry3Bb1 resistance, and to assess the reduction in adult emergence attributable to DvSnf7 and other traits. Insect resistance models were used to assess durability of SmartStax and SmartStax PRO to WCR resistance.

Results: …

Nematodes Associated With Mammals In The Great American Biotic Interchange (Gabi), F. Agustin Jimenez, Juliana Notarnicola, Scott Lyell Gardner

Scott L. Gardner Publications

The Great American Biotic Interchange (GABI) is a large-scale zoogeographic event that illustrates the exchange and diversification of mammals between North and South America. This phenomenon was accelerated by the connection of both landmasses during the Pliocene. Support for this phenomenon includes the extant distribution of xenarthrans, didelphiomorph marsupials, hystricognath and cricetine rodents, sciurids and carnivores, as well as the distribution of fossils in the stratigraphic record and the coalescence of genotypes. Contrasting with the relatively well-documented role and history of mammals in GABI, the role of their parasites has been largely neglected. As a consequence, the reconstructions of the …

Phytophagous Insect Oviposition Shifts In Response To Probability Of Flower Abortion Owing To The Presence Of Basal Fruits, Shivani Jadeja, Brigitte Tenhumberg

School of Biological Sciences: Faculty Publications

Phytophagous insects use a wide range of indicators or associated cues to avoid laying eggs in sites where offspring survival is low. For insects that lay eggs in flowers, these unsuitable sites may be created by the host plant’s resource allocation to flowers. In the sequentially flowering host plant, Yucca glauca, late-opening distal flowers are more likely to be aborted in the presence of already-initiated basal fruits because they are strong resource sinks. If flowers are aborted, all eggs of the phytophagous insect, Tegeticula yuccasella, within the flower die. We used the phytophagous insect T. yuccasella that lays …

Rewiring Metabolism Under Oxygen Deprivation: Naked Mole-Rats Evolved A Means To Cope With Anoxia, Jay F. Storz, Grant B. Mcclelland

Jay F. Storz Publications

When faced with a reduced availability of oxygen in the environment (hypoxia), vertebrates can make a variety of respiratory, cardiovascular, and hematological adjustments to ensure an uninterrupted supply of oxygen to the cells of metabolizing tissues (1, 2). These are adaptive solutions for “aerobic organisms in an aerobic world” (3). Coping with the complete absence of oxygen (anoxia) requires more fundamental alterations of cellular metabolism that are typically nothing more than emergency stopgap measures to buy time until the oxygen supply is (hopefully) reestablished (4). On page 307 of this issue [Science 356 (6335)], Park et al. (5) identify a …

Biotic Interchange Has Structured Western Hemisphere Mammal Communities, Danielle Fraser, S. Kathleen Lyons

School of Biological Sciences: Faculty Publications

Aim.— Many hypotheses posit that species-rich tropical communities are dominated by speciesspecies interactions, apparent as competitive exclusion or character displacement, whereas species-poor temperate communities are dominated by species-environment interactions. Recent studies demonstrate a strong influence of macroevolutionary and biogeographic factors. We simultaneously test for the effects of species interactions, climate, and biotic interchange on Western Hemisphere mammal communities using a phylogenetic and functional diversity approach.

Location.— Western Hemisphere.

Time period.— Modern

Major taxa studied.— Mammalia

Methods.— Using Western Hemisphere mammal distributional and body mass data, we calculate body mass dispersion, phylogenetic diversity (Net Relatedness Index), and assemblage-averaged rates of co-occurrence …

Palynological Investigation Of Mummified Human Remains, Karl Reinhard, Marina Milanello Do Amaral, Nicole Wall

Karl Reinhard Publications

Pollen analysis was applied to a mummified homicide victim in Nebraska, U.S.A., to determine the location of death. A control sample showed the normal ambient pollen in the garage crime scene. Ambient windborne types, common in the air of the region, dominated the control. Internal samples were analyzed from the sacrum, intestine, and diaphragm. Microfossils were recovered from the rehydrated intestine lumen. The intestinal sample was dominated by Brassica (broccoli). The sacrum sample was high in dietary types but with a showing of ambient types. The pollen from the diaphragm was dominated by ambient pollen similar to the control samples. …

Impact Of Disease On The Survival Of Three Commercially Fished Species, John M. Hoenig, Maya L. Groner, Matthew W. Smith, Wolfgang K. Vogelbein, David M. Taylor, Donald F. Landers Jr., John T. Swenarton, David T. Gauthier

Biological Sciences Faculty Publications

Recent increases in emergent infectious diseases have raised concerns about the sustainability of some marine species. The complexity and expense of studying diseases in marine systems often dictate that conservation and management decisions are made without quantitative data on population-level impacts of disease. Mark-recapture is a powerful, underutilized, tool for calculating impacts of disease on population size and structure, even in the absence of etiological information. We applied logistic regression models to mark-recapture data to obtain estimates of disease-associated mortality rates in three commercially important marine species: snow crab (Chionoecetes opilio) in Newfoundland, Canada, that experience sporadic epizootics …

Short-Term Effects Of Nutrients On A Barrier Island Grassland Community, Ashley Moulton

Theses and Dissertations

Increased nutrient availability globally has the potential to affect community functional composition of plants in nutrient limited environments, such as coastal grassland systems. Stability of these systems are threatened worldwide by urbanization, as well as effects of sea level rise and increased frequency and intensity of storms, and atmospheric N deposition, associated with climate change. Annual net primary productivity (ANPP), species composition, and functional traits (community weighted specific leaf area (CWSLA), leaf area index (LAI), growth form and photosynthetic pathway) were measured across four treatments to assess multiple resource limitation of nitrogen (N) and phosphorus (P) and functional community response …

Effects Of Prescribed Fire On Cope’S Gray Treefrog (Hyla Chrysoscelis) Across Habitat Scales And Life Stages, Logan Mcdonald

Theses and Dissertations

Fire may alter both aquatic and terrestrial habitat used by all amphibian life stages, yet, our knowledge of its effects on amphibians is primarily limited to adult responses. I present an integrated approach to test the response of Cope’s Gray Treefrog (Hyla chrysoscelis) to fire by examining responses in tadpole performance and survivorship, adult abundance, and oviposition. Tadpoles raised with burned leaf litter had similar survival, but total mass and total length were 440% and 170% greater, respectively, for tadpoles raised in unburned litter. I assessed terrestrial and aquatic oviposition cues by embedding burned and unburned litter treatments within burned …

A Comparative Analysis Of Geometric Morphometrics Across Two Pseudemys Turtle Species In East Central Virginia, Kristin C. Dillard

Theses and Dissertations

The phylogeny of the turtle genus Pseudemys is poorly understood. In Virginia, many turtles have been found with indicator traits of both eastern river cooters (Pseudemys concinna concinna) and northern red bellied cooters (Pseudemys rubriventris). This study explores morphological evidence for hybridization between the two species across three riverine sites in east central Virginia.

Museum voucher groups for each species were analyzed for relative shell height and plastron length. The shape of the plastral scutes and upper jaw were analyzed using landmark-based morphometric software. These metrics were compared with measurements taken from 188 field-caught Pseudemys specimens. …

The Soundscape Of The St. Johns River And Its Potential Impacts On The Habitat Use Patterns Of Bottlenose Dolphins, Carissa Deeann King

UNF Graduate Theses and Dissertations

The development of effective management plans for animal populations relies on an understanding of how the population is utilizing the habitat as well as the identification of any critical habitat areas. The St. Johns River (SJR), an urban estuary with a high level of anthropogenic disturbance, is home to a resident population of bottlenose dolphins (Tursiops truncatus). In chapter one, SJR dolphin habitat use patterns, the factors that influenced these patterns, and the critical habitat areas were identified. Significant associations were found in most pair-wise comparisons between season, behavioral state, group size, water depth, and location, indicating that …

Quantifying Current Sediment Deposition, Legacy Sediments, And Pre-Impoundment Vertical Accretion And Carbon Dynamics Following Dam Removal In A Recently Restored Tidal Freshwater Wetland, Melissa J. Davis

Theses and Dissertations

Damming disrupts natural sediment flow to downstream resulting in legacy sediment accumulation. Legacy sediments have been well investigated in streams throughout the Piedmont region; however, there is no research of legacy sediments following dam removal in low-gradient Coastal Plain streams. Research objectives were to: characterize legacy sediments in a low-gradient stream restoration, quantify pre-impoundment accretion and carbon dynamics, and assess current sediment deposition rates via ¹⁴C analyses within sediment cores and sediment collection tiles. Carbon accumulation and accretion rates of modern tidal sediment have reached that of the tidal relic benchmark and current sediment deposition rates are similar between …

Persistence Of The Larval Environment On Post-Metamorphic Performance And Population Dynamics In Amphibians, Julie Charbonnier

Theses and Dissertations

Organisms with complex life cycles may experience diverse stressors during their development. Stressors experienced in early life stages may influence the quantity and quality of individuals in later life stages. However, it is unclear if these effects persist later in life and how they may influence population dynamics. This dissertation uses two amphibian species, the Western spadefoot toad (Pelobates cultripes) and the spotted salamander (Ambystoma maculatum) to explore how biotic and abiotic factors experienced in aquatic and terrestrial environments influence phenotype and survival. We use a combination of field mesoscosm studies, laboratory studies and modeling to …

Effects Of Silencing Cyc2-Like Genes On Floral Development In Solanum Lycopersicum L. And Nicotiana Obtusifolia M. Martens & Galeotti (Solanaceae), Joonseog Kim

Theses and Dissertations

CYCLOIDEA (CYC) and DICHOTOMA (DICH) of the CYC2 clade of the TCP gene family have been shown to play a significant role in regulating the identity of the dorsal petals and abortion of the single dorsal stamen in Antirrhinum majus. It is believed that CYC2-like genes are responsible for the convergent evolution of floral zygomorphy, but their role in the development of actinomorphic flowers is still unknown. In Solanaceae, previous analysis has identified two paralogs of CYC2-like genes, CYC2A and CYC2B, resulting from a gene duplication that predates the origin the family. …

Evolution Of Antagonistic Relationships In Proteins: A Case Study Of Radialis- And Diviricata-Like Genes, Ao Gao

Theses and Dissertations

The antagonistic relationship of proteins describes the opponent interactions that result in one protein suppressing the function of another. Developmental genetic studies of Antirrhinum majus demonstrated that two transcription factors from the MYB gene family, RAD and DIV, interact through antagonism to regulate floral dorsoventral asymmetry. Interestingly, similar antagonistic interactions were found among proteins of FSM1 (RAD-like), MYBI (DIV-like), and DRIF in Solanum lycopersicum, which is involved in fruit development. Here, we report on the homology of these antagonistic MYB proteins based on reconstruction of the phylogeny of I-box-like and R-R-type clades, where RAD- and DIV-like belong, …

The Status Of Snapping Turtles (Chelydra Serpentina) In Virginia: Population Viability, Demography, Regulatory Analysis, And Conservation, Benjamin C. Colteaux

Theses and Dissertations

Snapping turtles (Chelydra serpentina) are being harvested in unprecedented numbers in the United States (US) to meet the needs of international markets. Over three million live snapping turtles from farm and wild caught stock were exported from the US to Asia in 2012-14 alone. In the Commonwealth of Virginia, records indicate that 29,860 snapping turtles were commercially harvested between 2000 and 2015. Size limits are often used to regulate harvest pressure in snapping turtles and other game species. I analyzed the historic harvest of eleven US states to test the efficacy of minimum-size limit regulations at reducing commercial …

The Role Of Habitat Management In Shaping Predation, Animal Color, And Gene Flow In A Metapopulation Of Florida Scrub Lizards (Sceloporus Woodi), Richard William Orton

College of Graduate Studies: Theses & Dissertations

Anthropogenic disturbance is known to affect biological diversity at the community, species, and genetic levels. Habitat fragmentation, in particular, has been shown to impact predator abundance and distribution, impede dispersal, and augment genetic drift. In small populations, which often result from habitat fragmentation, the effects of human disturbance may be disproportionately expressed. Small populations are more susceptible to selection pressures and random drift because genetic and phenotypic frequencies can become rapidly fixed, in comparison to larger populations. In turn, fixation of maladaptive alleles or morphs can accelerate extinction. For example, cryptic color polymorphism can be maintained by apostatic selection, where …

Silver Nanoparticle Fate And Accumulation In The Aquatic Food Web Of Stream Microcosms, Stefan J. Petersen

College of Graduate Studies: Theses & Dissertations

Silver nanoparticles (AgNPs) are used in 25% of all nano-enabled products and applied for anti-microbial properties. Silver nanoparticles are discharged into aquatic environments through wastewater discharge, runoff, and chemical spills. Once in aquatic environments silver nanoparticles have the potential to harm aquatic organisms. While the fate of silver nanoparticles in lentic systems has been investigated, limited information is available for the fate of silver nanoparticles in flowing environments. The purpose of this study was to compare the fate of AgNPs following a one-time pulsed application simulating a chemical spill, or small repetitive applications simulating effluent discharge, in artificial stream communities …