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Unraveling The Paradox Of The 'Great Speciators': Evolutionary Dynamics Of A Geographic Radiation Of Island Kingfishers (Todiramphus), Jenna Merle Mccullough

Biology ETDs

The paradox of the ‘Great Speciators’ describes a biogeographic pattern in which geographically widespread lineages have strong overwater dispersal capabilities, yet exhibit genetic and phenotypic divergence between islands, suggesting limited dispersal and cessation of gene flow. In my dissertation, I leveraged whole genomes and two comprehensive trait datasets of dispersal ability and plumage coloration of all described diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic ‘Great Speciators.’ Chapter 1 reveals that whole genome datasets do not outright solve the evolutionary relationships of this clade and that widespread incomplete lineage sorting (ILS) and gene flow are sources of …

Soil Bacterial Community Shifts In A Montane Longleaf Pine Restoration Site: Effects Of Dominant Herbaceous Species Removal, Prescribed Burn, And Changes In Season, Isabella K. Vahle

Master's Theses

Longleaf pine (Pinus palustris Mill.) ecosystems are one of the most endangered and ecologically diverse systems in North America. The native herbaceous species serve as fuel for low-intensity, recurring fires this system relies on. The herbaceous species play major roles in maintaining ecosystem structure and diversity. Soil microorganisms like bacteria are known to aid greatly in many different plant and ecosystem processes. However, little is known about the dominant herbaceous species and soil bacterial compositions within montane longleaf pine ecosystems, especially before and after a prescribed fire. We completed a multiyear, seasonal analysis of the soil bacterial community in …

Bioinformatic Comparison And Salinity Tolerance Of Various Cyanobacterial Strains, Lucie Rowe

Honors Theses

Cyanobacteria are an abundant and diverse group of photosynthetic prokaryotes with a long evolutionary history, which presents challenges for comprehensive taxonomic classification. Phylogenies were traditionally constructed based on the highly conserved 16S rRNA gene, but research has increasingly relied upon whole genome sequencing to elucidate evolutionary relationships, despite increased cost and time. In this thesis, publicly available genome sequences of various cyanobacterial strains were utilized to determine if the whole rRNA region, which includes the 16S, 23S, and 5S genes as well as the spacer regions between, could provide accurate, yet cost/time efficient representations of their evolutionary relationships. From phylogenetic …

Greening The Edge: Investigating Riparian Buffer Restorations In A Pastoral Setting And Their Effects On Soil Carbon And Microbial Community Composition., Seth Mccullough

Masters Theses, 2020-current

Riparian buffer restoration represents a critical strategy for enhancing ecosystem health and resilience in agricultural landscapes. This study investigates the effects of riparian buffer restoration on soil properties, microbial communities, and carbon dynamics in Rockingham County, VA. Through a comprehensive field study, we assessed the physicochemical properties of soil, microbial biomass, community composition, and soil carbon storage in restored and unrestored riparian buffers. Our findings reveal significant improvements in soil physical properties in restored buffers, including increased soil moisture (p < 0.05) and decreased bulk density (p < 0.01), indicating enhanced soil structure and water retention capacity. While no significant differences were detected in soil pH or cation exchange capacity, restored buffers exhibited higher soil carbon stocks (p < 0.05) and carbon-to-nitrogen ratios, suggesting potential differences in nutrient cycling processes and organic matter decomposition rates. Moreover, restored buffers showed increased microbial biomass (p < 0.01), potentially driven by improved habitat conditions and shifts towards a fungal-dominated microbial community.

Although no significant differences were found in overall microbial community composition between restored and unrestored sites, specific shifts in bacterial …

Selection During Reproduction In Mimulus Guttatus, Desmond C. Willson, Karla De Lima Berg, Mitch Cruzan

Student Research Symposium

A lack of genomic studies examining gametophytic selection and selective embryo abortion—which occur during the reproduction of angiosperms—leaves questions regarding the adaptive and evolutionary effects of these processes. Analyzing deviations from Mendelian segregation offers an avenue for identifying loci targeted by GS and SEA, and their contributions to purging of genetic load. However, other selective processes such as meiotic drive and cytonuclear interactions, as well as pollen and ovule abortion, can cause distortion. To distinguish the effects of GS and SEA from other causes of distortion, we will perform reciprocal crosses between highly homozygous and highly heterozygous individuals of Mimulus …

Relationship Between Trunk Cross-Sectional Area Growth And Water Stress In Garry Oaks (Q. Garryana): A Species Of Conservation Concern, John Cochrane

Student Research Symposium

In the Pacific Northwest, Quercus garryana (Garry oak trees) support over 627 native species. Garry oak natural habitat was originally maintained by indigenous practices but has been reduced to 5-10% of its range due to change in land management strategies. To support oak conservation, we need to understand heat and water affect the growth and physiology of this species. In this study, we created a fixed linear model of trunk cross-sectional growth with water stress (Ψ), photosynthetic water-use efficiency (δ¹³C), and leaf Carbon-Nitrogen ratio. We collected branch samples from the canopies of 47-64 mature Garry oaks in the …

Phytoplankton Community Dynamics In The Northern California Current System, Kristin Forgrave

Student Research Symposium

The Northern California Current system is a productive coastal ecosystem that encompasses a variety of temporal and spatial features. The photosynthetic microbial community plays a crucial role in supporting the rich ecosystem and economically important fisheries. My research integrates data across distance and two years to investigate the community composition of two major phytoplankton groups in this system: picocyanobacteria and picoeukaryotes. The abundances and sizes of the phytoplankton were measured using flow cytometry. Picoeukaryotes were found to be present at similar concentrations in both summer and winter. Abundances of both cell types were comparable in the winter, but picocyanobacteria were …

Reef Ecosystem Conservation For The Hawaiian Islands: The Impacts Of Ocean Warming And Acidification On Benthic Reef Populations, Samantha Roberts

Student Theses 2015-Present

This paper explores the anthropogenic effects of rapid climate change and ocean acidification on benthic coral populations along the Hawaiian archipelago. Moreover, the reliance of Hawaiian coastal communities on coral reefs for sustenance and economic prosperity is evaluated to determine the importance of reef ecosystem conservation for the prosperity of Hawaii. Chapter 1 introduces the importance of coral and supplies quantitative data on declining coral populations traditional to Hawaii, as a result of ocean warming and acidification. Empirical data from prior, prominent studies, combined with my own, will be discussed. Chapter 2 outlines the ecology of Hawaiian reef ecosystems, the …

Ancient Wisdom, Modern Prosperity: Harnessing Traditional Ecological Knowledge To Revitalize Australia's Economy, Environment, And Human Wellbeing, Annabelle L. Baulch

Student Theses 2015-Present

This paper explores the traditional knowledge of Australia’s Indigenous people and how it can improve Australia's environment, health, and economic prosperity to shape a more sustainable future. Indigenous Australians managed the land for thousands of years; however, being forced off the land following European colonization resulted in terrible cultural, social, and environmental disruption for Aboriginal Australians and made conservation efforts difficult. Wildfires, imported species, mining, and agriculture is steadily destroying the Australian ecosystem, contributing to climate change, species extinction, and gaps in our cultural and ancestral knowledge. Chapter One overviews Australia's environmental issues; it uses quantitative data to explore the …

Crossing The Ocean: The Importance Of Gene Flow In Island Evolution, Ethan F. Gyllenhaal

Biology ETDs

Islands have long been a critical arena for the development of ecological and evolutionary theory, particular due to persistent open-water gaps between them. In this dissertation I demonstrates how these caps are permeable, which can be leveraged to understand evolution on islands and more broadly. The first chapter develops this connection between ongoing, overwater gene flow and island biogeographic theory, and tests it on an archipelago species. The second take a three-pronged approach in demonstrating how over-water gene flow can bias phylogenetic inference, and how many phylogeographic metrics in islands are likely shaped by long-term gene flow. The final two …

Researching Covid To Enhance Recovery (Recover) Pediatric Study Protocol: Rationale, Objectives And Design, Rachel S. Gross, Tanayott Thaweethai, Erika B. Rosenzweig, James Chan, Lori B. Chibnik, Mine S. Cicek, Amy J. Elliott, Valerie J. Flaherman, Andrea S. Foulkes, Margot Gage Witvliet, Richard Gallagher, Maria Laura Gennaro, Terry L. Jernigan, Elizabeth W. Karlson, Stuart D. Katz, Patricia A. Kinser, Lawrence C. Kleinman, Michelle F. Lamendola-Essel, Joshua D. Milner, Sindhu Mohandas, Praveen C. Mudumbi, Jane W. Newburger, Kyung E. Rhee, Amy L. Salisbury, Jessica N. Snowden, Cheryl R. Stein, Melissa S. Stockwell, Kelan G. Tantisira, Tamara Bradford, Et Al

School of Medicine Faculty Publications

Importance The prevalence, pathophysiology, and long-term outcomes of COVID-19 (post-acute sequelae of SARS-CoV-2 [PASC] or “Long COVID”) in children and young adults remain unknown. Studies must address the urgent need to define PASC, its mechanisms, and potential treatment targets in children and young adults. Observations We describe the protocol for the Pediatric Observational Cohort Study of the NIH’s REsearching COVID to Enhance Recovery (RECOVER) Initiative. RECOVER-Pediatrics is an observational meta-cohort study of caregiver-child pairs (birth through 17 years) and young adults (18 through 25 years), recruited from more than 100 sites across the US. This report focuses on two of …

Fecal Genomics Provides Insights On Connectivity Of Endangered Wildlife In A Human Dominated Landscape, Abhinav Tyagi

Theses and Dissertations

Many mammalian species, facing severe historic range reductions, now inhabit fragmented habitats. Habitat fragmentation involves the reduction of habitat into smaller patches, increasing distances between them, and eventually leading to small isolated populations. Species' responses to habitat alteration may vary based on factors such as body size, dispersal ability, and abundance. Understanding these differences is crucial for effective multispecies conservation planning. Genomic data, within a landscape genetic framework, are increasingly applied to evaluate the effects of habitat fragmentation and understand influential landscape features for connectivity. The quantity of data enhances the power and precision of assessing landscape impacts on gene …

Lmpact Of Salmonella Enterica Effector Proteins On Plant Physiology And Immunity, Sara Qader

Honors Theses

Salmonella enterica serovar Typhimurium are primarily recognized as pathogens associated with foodborne illnesses in humans. Salmonella also can colonize plant tissue effectively. The pathogen relies on type III secretion systems (T3SS) to infect mammals and plants successfully and counteract the immune response. Understanding the molecular mechanisms underlying Salmonella’s interactions with plants is essential for developing effective strategies to reduce its impact on human health and agriculture. Effector proteins, known for their role in modulating host-pathogen interactions, have been implicated in the virulence and pathogenicity of Salmonella. However, their specific functions and contributions to Salmonella’s interactions with plants remain largely unknown. …

Riparian Expansion Post-Restoration Efforts Along The Upper Clark Fork River, Makena Tanko

Graduate Theses & Non-Theses

Floodplain restoration is an intricate process aimed at promoting water quality, biodiversity, and maintaining ecological balance. However, mapping vegetation patterns on a restored floodplain can be challenging due to different geomorphic locations across a river sections, including flooding regimes, sediment characteristics, elevation, and ground water availability. This study investigates the drivers of vegetation succession in floodplains post-restoration along the Upper Clark Fork River, encompassing Phases 1, 2, 3, and 5. We analyzed key factors influencing vegetation response, including total canopy cover and woody vegetation health, in comparison to soil compaction, geomorphic location, distance from streambank, time post-restoration, and metal levels …

Beating The Heat: The Use Of Coral-Benefitting Bacteria For Heat-Stressed Anemones And Inspiring Future Biologists, Navah Eshraghi

Undergraduate Honors Theses

The warming of ocean temperatures has caused mass coral-bleaching events characterized by the expulsion of vital algal symbionts from coral tissues. However, the possibility of algal reuptake and existence of bacteria that support coral-algal symbiosis are two avenues of potential restoration efforts. Using the sea anemone Exaiptasia diaphana as a model for corals, I tested whether the coral-benefitting bacterium Endozoicomonas montiporae could enhance algal uptake under ambient (27°C) and heat-stressed (32°C) conditions. I then turned acquired results into an article modeled after National Geographic Kids to introduce the experiment to younger ages. While temperature was a larger determinant of algal-uptake …

First Record Of The Invasive Chenopodium Aphid, Hayhurstia Atriplicis (Linnaeus, 1761) (Hemiptera: Aphididae), In Colombia, Takumasa Kondo, Roberto Rosero, Jackeline Gaviria

Insecta Mundi

The chenopodium aphid, Hayhurstia atriplicis (Linnaeus, 1761) (Hemiptera: Aphididae), is reported for the first time in Colombia. The aphid was found on the aerial parts of the quinoa plant, Chenopodium quinoa Willd. (Amaranthaceae), especially on the leaves, in five municipalities in the department of Cauca, Colombia. Brief information on its natural enemies, distribution and biology is provided. This is the only aphid in Colombia known to cause malformations on the leaves of quinoa plants. In South America, this aphid has been found previously only in Ecuador, where it was reported for the first time in 2023 based on specimens collected …

Three Additions To The False Click Beetle (Coleoptera: Elateroidea: Eucnemidae) Fauna In The Nearctic Region, Robert L. Otto

Insecta Mundi

Three species of false click beetles (Coleoptera: Eucnemidae) are added to the Nearctic fauna. One new species, Isorhipis bicolor, is described from a small series collected in Florida, U.S.A. Eighteen specimens collected from Georgia were identified as Dyscharachthis amplicollis (Fleutiaux), new U.S.A. records for a species previously taken from Japan and Southeast Asia. Examination of a series of eucnemids collected by Kyle Schnepp in Florida allowed me to revisit the Deltometopus fauna in eastern North America. Antennal structures present in a series of male specimens in the loan and past examined specimens are definitive enough to resurrect Deltometopus …

First Record Of The Beekeeping Pest Aethina Tumida Murray (Coleoptera: Nitidulidae) For Honduras, Jesus Orozco

Insecta Mundi

Aethina tumida Murray (Coleoptera: Nitidulidae) (also known as the small hive beetle), an important pest in apiaries, is reported from Honduras for the first time, new country record. The precise distribution in the country is unknown, and no damage related to it has been observed. Photographs are provided to aid in its identification. Differentiation of A. tumida from Aethina villosa Reitter and Aethina quadrata Sharp, which also occur in Honduras, is provided.

ZooBank registration. urn:lsid:zoobank.org:pub:DAF12C6A-0F8C-4151-9C4D-F191CCC4032F

The First Draft Genome Of Cold-Water Octocoral Anthothela Grandiflora, The Great Flowerbud Coral, Laurel Humphrey

Honors Scholar Theses

Cold-water corals are important sources of ocean biodiversity, yet populations are increasingly threatened by human activity and climate change. Soft octocorals may endure higher ocean acidification levels in comparison to stony hexacorals, although the mechanisms of octocoral biomineralization are less understood. Building genomic resources for cold-water octocorals could help to close information gaps by elucidating the evolutionary history of octocoral calcification and provide a reference for future studies of adaptation to acidified waters. This report describes the first reference genome for the cold-water octocoral species Anthothela grandiflora found throughout the Atlantic Ocean. Sequencing using Oxford Nanopore Technologies generated 43.6 Gb …

New Records Of Mesobuthus Rakhshanii Barahoei, 2022 In Iran (Scorpiones: Buthidae), Ersen A. Yağmur, Zhale Baghernavesi, Zahra Taherkhani, Parsa Akbari, Mohammad Moradi

Euscorpius

Mesobuthus rakhshanii Barahoei, 2022 (Scorpiones: Buthidae) was so far known only from the type locality in Sistan and Baluchestan Province, Iran. We give a list of numerous new records of this species from the same province. A map and detailed illustrations are provided.

Fiddler Crab Gut Microbiomes As An Indicator For Eutrophication Due To Waste-Water Contamination In Estuaries, Madison L. Geraci

Honors Theses

Estuaries are unique biogeochemical zones in coastal systems that provide a myriad of ecological functions: providing habitat for critically important fishery species, diverse species of plants and animals, and contributing to nutrient cycling. Estuaries are vulnerable to anthropogenic stressors as they are intersections between marine and terrestrial communities and are often the hotspot of coastal development and activity. Estuarine sediments act as repositories for anthropogenic contaminants, including excess nutrient runoffs and waste-water pollution that can cause states of eutrophication. Microorganisms are sensitive to these environmental changes, presenting a unique opportunity of being useful bioindicators of environmental stress. Isolating microorganisms from …

Impacts Of Urbanization On Demographics And The Stress Level Of White-Tailed Deer In The Piedmont Of South Carolina, Cameron Bramhall

Graduate Theses

Population demographics and density studies are a common way of determining number of individuals in location. Understanding how many individuals and sex ratios can help estimate total populations for future potential management practices. For white-tailed deer (Odocoileus virginianus), commonly referred to as whitetail deer, like other cervids, having too many or too few individuals in an area can cause issues. Some of the issues that may arise with too many individuals include higher disease potential, and a general lack of resources leading to an increase in competition. As areas that were once habitat for whitetail deer become more and more …

Threads Of Connection: An Offering To Re-Tangle Humanity And Nature With The Patterns Of Our World, Emily Shelton

Graduate Theses

In our world there are patterns of self-similarity that serve as evidence of the interconnectedness between humankind and the rest of the natural world. They are reflected in our bodies, behaviors, and environments, both natural and manmade, and can be found throughout systems at every scale, micro through macro. These organic, linear motifs branch into smaller iterations that seem to shape our existence on this planet as we gravitate towards experiences that echo these patterns. During everyday acts like shopping in a grocery store or a crowd at a concert, we unconsciously participate in self-similar collective movements as we navigate …

West Coast Rock Lobster Resource Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries Management Papers

Harvest strategies for Western Australia’s (WA) aquatic resources are formal documents developed by the Department of Primary Industries and Regional Development (DPIRD, the Department) to support decision-making processes that ensure the outcomes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002a) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). Harvest strategies are a key component of all contemporary fishery management systems and a requirement for certification under the Marine Stewardship Council (MSC). The objectives of ESD are reflected in the objectives of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act …

Random-Effects Substitution Models For Phylogenetics Via Scalable Gradient Approximations, A. F. Magee, A. J. Holbrook, J. E. Pekar, Itzue W. Caviedes-Solis, F. A. Matsen Iv, G. Baele, J. O. Wertheim, X. Ji, P. Lemey, M. A. Suchard

Biology Faculty Works

Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate …

Reconnecting With Nature One Classroom At A Time, Bianca Apuzzo

Senior Honors Projects

Environmental science is more important to today’s society than it has ever been, and developing basic ecoliteracy is the easiest way we can work towards a more sustainable future. Ecoliteracy allows us to connect deeper to nature and provides us with the information needed to protect and restore our beautiful planet. We are rolling downhill, picking up speed as we go, through a silent mass extinction. The scariest part of it all: nobody seems to care.

In response to the lack of environmental education provided to today’s students, I have created a syllabus for a high school level science course …

Invasive Shrubs Differentially Alter Autumnal Activity For Three Common Small-Mammal Species, Brian M. Connolly, Chad Zirbel, Carson Keller, Mark Fuka, John L. Orrock

Biology Faculty Scholarship

Seasonal variation in animal activity influences fitness and the intensity of ecological interactions (e.g., competition, predation), yet aspects of global change in the Anthropocene may catalyze shifts in seasonal activity. Invasive plants are components of global change and can modify animal daily activity, but their influence on animal seasonal activity is less understood. We examined how invasive woody shrubs (Autumn olive [Elaeagnus umbellata] and Amur honeysuckle [Lonicera maackii]) affect seasonal activity of three common small-mammal species by coupling experimental shrub removal with autumnal camera trapping for two consecutive years at six paired forest sites (total 12 …

Identifying Grassland Cores In The Southeast: Relating Spatial Covariance To Avian Communities And Vegetation Structure, Lauren L. Berry

Graduate Theses and Dissertations

Globally, grasslands are declining in range, which is leading to a decline in grassland-dependent taxa. These declines can be attributed to a variety of issues, a major one being the encroachment of woody species into historic grasslands. There is a new framework for strategizing grassland management, referred to as “Defend the Core,” which calls for proactive management of intact grasslands, meaning conserving remaining grasslands by preventing woody encroachment in the first place. To successfully defend the core, it is imperative that we develop rapid methods to identify intact grassland cores for management priority. One method that can be used for …

Migration And Breeding Ecology Of King Rails (Rallus Elegans) In Southeast Arkansas, Jessica Schmit

Graduate Theses and Dissertations

King Rails (Rallus elegans) are a secretive marsh bird species of conservation concern in Arkansas. Freddie Black Choctaw West WMA in southeast Arkansas has multiple confirmed pairs of breeding King Rails and offered an opportunity to investigate King Rail migration ecology, as well as nesting ecology and nest site selection. In Chapter 1, we determined migratory status (resident vs. migratory) and described seasonal movement. To do this, we captured and outfitted 23 birds with Argos GPS tags to track migration patterns throughout the season. We found that most of the population did not make long distance migrations but instead were …

Bilateral Asymmetry In The First Metacarpal: The Influence Of Handedness In Humans And Non-Human Primates, Lucyna A. Bowland

Graduate Theses and Dissertations

Muscle attachment sites (entheses) are often used to infer soft tissue anatomy and reconstruct behaviors within skeletal populations, but there remains a significant debate about whether and to what degree muscle use is accurately reflected in bony morphology. One of the most difficult problems in establishing the relationship between variation in muscle use and entheseal development is the inability to exclude a variety of external factors thought to influence enthesis development, including age, sex, body mass, and activity patterns. One way around this is to take advantage of the fact that humans are handed (preferentially using one hand over another, …