Digital Commons Network^™

The Micro-Communities Of Trees, Nicholas Davis, Lily Boysworth, Westen Wilburn

Fall Showcase for Research and Creative Inquiry

This study investigated how tree species diversity influences the variety of organisms living on or around trees across different habitat types. Field data were collected through random tree selection, measurement of tree diameter, identification of species, and estimation of surrounding ground cover types such as grass, herbaceous plants, woody plants, and leaf litter. Biodiversity associated with each tree was analyzed using the Shannon Diversity Index across several ecosystems, including grassland, woodland, and pond environments. Results indicated that the pond ecosystem exhibited the highest species diversity, followed by woodlands and then forests. A range of organisms, including lichens, mites, fungi, and …

Dusky Grouse Seasonal Resource Selection In The Great Basin Isolated Mountain Ranges Of Nevada, Usa, Stephanie Landry, Brian Smith, Erica Stuber, Shawn Espinosa, David Dahlgren

Aspen Bibliography

Dusky grouse Dendragapus obscurus are a montane forest grouse species with a paucity of information regarding their temporal and spatial resource use during critical times of high mortality and reproductive output. This lack of vital data may leave dusky grouse at risk of sub-optimal management in many areas of their distribution, especially in the isolated ‘sky island’ mountain ranges of the Great Basin, where high elevation habitats are surrounded by sagebrush and salt desert shrub land flats. Many of these high elevation habitats are being altered and lost rapidly from increasing disturbance events and effects of climate change. Our objective …

Phylogenetic Comparative Vocal Evolution, Casper W. Buchanan

Master's Theses

Vocal learning is a trait unique to humans, bats, cetaceans, primates, and birds (Jarvis & Nottebohm, 1997; McComb & Semple, 2005; Wilbrecht & Nottebohm, 2003). Although there has been extensive research on vocal learning in songbirds, parrots are an even closer proxy to human learning, as they are social, intelligent, and lifelong learners, with some having repertoires of over 300 sounds (Benedict et al., 2022; Péron et al., 2011; Thomsen et al., 2019; Toft & Wright, 2015). Elevated vocal learning can be attributed to the need for parrots to have strong communication skills through the sharing of information over foraging, …

Living Shoreline Prioritization And Hydrodynamic Habitat Suitability Models For Restoration In The Indian River Lagoon And Lake Worth Lagoon, Florida, Kelly M. Kibler, Melinda J. Donnelly, Vincent Encomio, Madison Giuntoli, Manisha Thenuwara, Brice Bennett, Laura Andrade Barron, Mariam Sonbol, Wynter Raine Seppala, Namritha Ramakrishnan, Jennifer Jordan Báez, Beth Orlando, Irene Arpayoglou, Melissa Meisenburg

Indian River Lagoon Shorelines

The spatial dataset: UCF_shorelinemodel_IRL_LWL.shp, was created with support from the Indian River Lagoon National Estuaries Program and Florida Sea Grant. These projects cumulatively led to creation of a living shoreline restoration prioritization model and hydrodynamic habitat suitability models for 1,550 km (963 miles) of estuarine shorelines in Indian River Lagoon and Lake Worth Lagoon.

The dataset presented herein includes:

1. shoreline data from >15,000 transects collected in the field,
2. shoreline wave climate data created through hydrodynamic modeling and frequency analysis of historic data,
3. categorization of potential risk for shoreline boat wake impact,
4. persistence of seagrass within 210 m of the shoreline, …

‘Earth System Engineers’ And The Cumulative Impact Of Organisms In Deep Time, Simon A. F. Darroch, Michelle M. Casey, Alison T. Cribb, Amanda E. Bates, Matthew E. Clapham, Dori L. Contreras, Matthew Craffey, Ivo A. P. Duijnstee, William Gearty, Nicholas J. Gotelli, Marcus J. Hamilton, Riley F. Hayes, Pincelli M. Hull, Daniel E. Ibarra, V. A. Korasidis, Jaemin Lee, Cindy V. Looy, Tyler R. Lyson, Benjamin Muddiman, Peter D. Roopnarine, Alex B. Shupinski, Felisa A. Smith, Alycia L. Stigall, Catalina P. Tomé, Katherine A. Turk, Amelia Villaseñor, Peter J. Wagner, Steve C. Wang, S. Kathleen Lyons

College of Life Sciences Faculty Papers

Understanding the role of humans as 'ecosystem engineers' requires a deep-time perspective rooted in evolutionary history and the fossil record. However, no conceptual framework exists for studying the rise of ecosystem engineering in deep time, requiring us to consider effects that fall outside the scope of traditional definitions. Here, we present a new framework applicable to both modern and ancient engineering-type effects. We propose a new term - 'Earth system engineering' - to describe biological processes that alter the structure and function of planetary spheres, and which combines core tenets of ecosystem engineering, niche construction, and legacy effects. We illustrate …

Detection And Classification Of Invasive Callery Pear From Multisource Satellite Imageries In Google Earth Engine, Kavi Raj Awasthi, Nilesh Timilsina, Denita Hadziabdic, Federico Iuricich, William E. Klingeman, Marcin Nowicki, Brook T. Russell, Jessica A. Hartshorn

Publications

Assessing the spatial distribution of invasive species is a critical component for establishing baselines to examine the rate of spread, documenting key areas where negative impacts on ecosystems can be mitigated, and developing sustainable management strategies. Callery pear (Pyrus calleryana Decne.; PC) is a rapidly spreading invasive woody plant species in the eastern United States (U.S.). The incursion of these wild-type trees into urban, peri-urban, and rural landscapes, which have escaped from transplanted clonal cultivars, poses complex management challenges for land managers and hampers ecosystem function by competing with native plant species and altering the forest environment. We integrated …

Multilevel Selection In The Margins: A Review Of Its Representation In Undergraduate Biology Textbooks, C. A. Greene, S. J. Mcpeek, L. Mitchem, A. B. Clark, Vincent A. Formica

Biology Faculty Works

Multilevel selection (MLS) is a foundational framework that expands the concept of natural selection beyond the traditional focus on individuals or genes to larger units, like groups. Despite strong empirical support and applications in a broad range of biological fields, MLS, often referred to as group selection, has a controversial history, which has impeded its wide use and led to incorrect inferences on the sources and strength of selection. Here, we explore how MLS is currently presented to undergraduate biology students by analyzing the content of nine commonly used Evolutionary Biology and Animal Behavior textbooks. We ask whether and how …

Using Rattlesnake Venom To Model Complex Trait Evolution Across Ecological And Evolutionary Scales, Samuel R. Hirst

USF Tampa Graduate Theses and Dissertations

A central challenge in evolutionary biology is understanding how genetic variation leads to phenotypicdiversity, particularly for complex traits that strongly influence fitness. Traits form the substrate of natural selection, but it is genes, that are inherited across generations. To fully understand the evolutionary process, we must therefore connect the molecular basis of trait variation with the evolutionary outcomes of such traits.

For relatively simple traits, the genotype–phenotype relationship is well understood. Classic systems, such as coat color in beach mice or toxin resistance in garter snakes, have provided effective examples of how relatively few loci underlie conspicuous adaptive differences across …

Dramatic Biases In Terrestrial Nitrogen Fixation In Earth System Models Revealed By Natural Isotope Signatures, Maoyuan Fang, Shushi Peng, Philippe Ciais, Daniel S. Goll, Benjamin Z. Houlton, Ying-Ping Wang, Yilong Wang, Pan Liu, Joshua B. Fisher, Pierre Regnier

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Biological nitrogen fixation (BNF) is the primary input of new reactive nitrogen to natural terrestrial ecosystems. However, this flux is poorly constrained due to its unclear drivers and associated control mechanisms. Here, we extend the existing theory of nitrogen (N) isotope mass balance to estimate BNF rates and then use a Bayesian approach to constrain the BNF rates in natural terrestrial ecosystems by using measurements of natural N-isotope ratios (δ¹⁵N) in plants (δ_P) and soil (δ_S). Together with pairwise δ_P and δ_S measurements from 18 forest sites covering diverse climates and thousands …

Genetic Characterization And High-Resolution Total Mrna Sequencing Of The Millipede Cherokia Georgiana Bollman, 1889, Elena Cruz

Biology Theses

There are approximately 12,000 described species within the class Diplopoda. Only six species, falling within four of sixteen orders, have fully sequenced genomes. No whole genomes are available for incredibly diverse families like Xystodesmidae. Many interesting characteristics in this group are poorly defined at the genetic level, such as the production of a defensive hydrogen cyanide secretion and UV fluorescence in the order Polydesmida. Here, we present a genetic characterization of the polydesmid millipede Cherokia georgiana Bollman, 1889. We include tissue-specific sequencing metrics, alignment and assembly of mitochondrial DNA consensus sequence according to tissue type, and phylogenetic tree construction using …

The Term Consciousness And Impressive Evidence For Cephalopod Awareness, Donald M. Broom

Animal Sentience

Mather presents comprehensive evidence of cephalopod cognitive ability and of a high level of awareness. The importance of taking account of the biological functioning and adaptations to the living environment is emphasised. An argument is presented that it is better to limit the use of the word conscious to ‘not unconscious’ and to use awareness in relation to the various levels of cognitive functioning.

The Consciousness Inherent In Chasing Your Tail, Sergio M. Pellis Dr.

Animal Sentience

Who is conscious and how do we know? Complexity in behavior and cognition is certainly a clue that cannot be ignored in identifying this trait, and as Mather’s target article shows, it is hard not to imagine consciousness arising in cephalopods. But how complex is complex? An alternative may be gleaned from the fact that all living things rely on negative feedback to navigate their worlds, and this requires all sentient beings knowing what is to be stabilized in reflection to themselves. If so, consciousness is a universal trait.

Sequestration Of Plant Defenses By Spotted Lanternfly (Lycorma Delicatula) And Effects On Avian Predators, Anne E. Johnson, Allison Cornell, Fang Zhu, Ashley E. Shay, Gabrielle Davis, Kelli Hoover

Biology Faculty Publications

Lycorma delicatula is a polyphagous phloem feeder, which is spreading rapidly in the U.S., and is a major threat to grapes, hops, and ornamentals. Among its hosts, L. delicatulaprefers Ailanthus altissima, an invasive tree from which it sequesters toxins, including several quassinoid compounds. We tested how these defenses affected predation by birds of nymphal and adult L. delicatula. Freeze-killed nymphs of each instar were reared with or without access to A. altissima and placed into cups on top of nest boxes occupied by house wrens (Troglodytes aedon). House wrens ate or fed their chicks a …

Limb Regeneration In Damselflies Based On Developmental Stage, Haven O. Clements

Inquiry: The University of Arkansas Undergraduate Research Journal

Injury is common in wild animals, yet some species possess an adaptive advantage: regeneration. Enallagma vesperum, a species of damselfly, exhibits this regenerative ability, though its persistence and effectiveness across developmental stages remain poorly understood. While previous studies indicate that regeneration ceases following adult emergence, it is unclear whether this ability also diminishes prior to the final larval molt. This study investigated the effectiveness of limb regeneration in E. vesperum across early and late larval instars. I hypothesized that earlier instars would exhibit greater regenerative success due to fewer competing energetic demands compared to later instars, which may prioritize …

Flawed Analysis Invalidates Claim Of A Strong Yellowstone Trophic Cascade After Wolf Reintroduction: A Comment On Ripple Et Al. (2025), Dan R. Macnulty, David Cooper, Michael Procko, T.J. Clark-Wolf

Aspen Bibliography

Ripple et al. (2025) recently argued that large carnivore recovery in Yellowstone National Park triggered one of the world’s strongest trophic cascades, citing a ∼1500 % increase in willow crown volume derived from plant height data. In this comment, we show that their conclusion is invalid due to fundamental methodological flaws. These include use of a tautological volume model, violations of key modeling assumptions, comparisons across unmatched plots, and the misapplication of equilibrium-based metrics in a non-equilibrium system. Additionally, Ripple et al. rely on selectively framed photographic evidence and omit critical drivers such as human hunting in their causal attribution. …

Consciousness Below Scuba Depths, Michael Vecchione

Animal Sentience

Abstract: Jennifer Mather has nicely summarized what is known about consciousness in shallow water octopods as well as what is known about shallow water squids and cuttlefish. However, once she gets below SCUBA depths, she misses out on most of cephalopod diversity. I have attempted to add this aspect and perhaps some evolutionary biology to this target article.

The Effects Of Plastic Mulch And Irrigation On Hemp Chemistry And Leaf Endophytes, Allison Rietman, Connor Morozumi, Robert C. Pearce, Natalie Christian

Journal of Agricultural Hemp Research

As an emerging crop, cultivation techniques for industrial hemp (Cannabis sativa L.) are still being developed and optimized. For example, irrigation and plastic mulching are some management practices that have been touted for their benefits in improving crop quality. Both techniques ensure ample water availability, which has often been attributed to improving hemp cannabinoid and terpene composition. In this study, we examined how supplemental irrigation implemented in a plastic mulch system influenced the cannabinoid and terpene profiles of one cultivar of CBD hemp, Lifter. We grew industrial hemp in field with plastic mulch and applied regular irrigation to one group …

Notes On Reproduction, Seasonality, And Roost Sites For Silver-Haired Bats (Lasionycteris Noctivagans) In Western Nebraska, Joseph W. Paysen, Dawson V. Kosmicki, Keith Geluso

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Silver-haired Bats (Lasionycteris noctivagans) are a migratory species found throughout the United States, southern Canada, and northern Mexico. Throughout their range, Silver-haired Bats roost in various tree species, generally within decaying features like cavities and exfoliated bark. Herein we report on additional reproductive and seasonal data as well as the first data on trees used as roost sites by Silver-haired Bats in Nebraska. We captured individuals along a small tributary of the North Platte River at Ash Hollow State Historical Park, Garden County, Nebraska, and tracked bats to their roosts. At this location, we documented lactation on 17 …

Attributes Of Artificial Wetlands Colonized By Ambystoma Maculatum On A Virginia Surface Mine, Hunter Hill, Garrett Stiltner, Walter H. Smith

Virginia Journal of Science

Landscapes impacted by surface mineral extraction present a range of artificial wetland habitats potentially useable by pool-breeding amphibians, although little information exists in the literature detailing which attributes influence breeding site selection by wetland amphibian specialists in post-mined landscapes. We compared attributes of artificial wetlands consistently used and unused as oviposition sites by Spotted Salamanders (Ambystoma maculatum) over a six-year period on a 120-ha former surface mine in Wise County, Virginia, USA. Salamanders non-randomly selected wetlands as oviposition sites, with one-third of available wetlands within the study area showing evidence of ovipositioning. Wetlands used as breeding sites were …

Attitudes Toward The Continued Protection Of Gray Wolves Under The Endangered Species Act, John A. Vucetich, Jeremy T. Bruskotter

Michigan Tech Publications

In February 2024, the U.S. Fish & Wildlife Service announced their intention to develop – for the first time – a National Recovery Plan under the Endangered Species Act (ESA) for gray wolves in the lower 48 states. In August 2025, a federal judge vacated the U.S. Fish and Wildlife Service's (FWS) decision denying ESA protections for gray wolves in the Western U.S.

Those events represent key context for this report, which describes the results of a web-based survey implemented in July and August of 2025 and designed to assess the attitudes of residents of the contiguous United States, as …

Mhc Gene Analysis And Immune Variation In Lepidodactylus Lugubris (The Mourning Gecko), Helen T. Vu

2025 Fall Honors Capstones Projects - Archive

The major histocompatibility complex (MHC) plays a central role in vertebrate immune defense by enabling pathogen recognition and initiating adaptive immune responses. While MHC diversity has been extensively studied in sexually reproducing species, comparatively little is known about its evolution in asexual lineages. The parthenogenetic gecko Lepidodactylus lugubris provides a unique opportunity to investigate how clonality and hybrid origins influence immune gene diversity. By leveraging whole-genome data, this study overcomes the limitations of previous transcriptome-based analyses and provides a more comprehensive view of MHC diversity in a clonal vertebrate. As the first step towards understanding MHC evolution in parthenogenetic lizards, …

Ecology Of Eupatorium Altissimum Galls: Extrapolating Timing Of Oviposition Using Plant Growth Curves, Tomofumi Inoue, Dana Dudle, James Benedix

Annual Student Research Poster Session

This study aims to investigate the timing of oviposition by the gall fly Neolassioptera perfoliata on tall boneset (Eupatorium altissimum) populations throughout the DePauw University Nature Park. I initially measured the heights of 176 plants total in 5 different locations, out of which I randomly selected 12-17 plants per location to measure height on a weekly basis. When galls were spotted, their heights were recorded so that they could be compared to the plant heights to produce an estimate for when the egg was laid by the gall fly. I also collected galls from plants that were excluded in the …

Zero Textbook Cost Syllabus For Env 3070 (Agroecology), Benjamin Iuliano

Open Educational Resources

Our relationships with the food we eat are deeply personal, but also connect us to a wide array of people, plants, animals, and landscapes around the world. Encompassing a diversity of scholarly approaches, the field of agroecology seeks to understand the interactions among these components, draw attention to the consequences of our present industrial food system, and create the conditions for more sustainable and just futures. In this course, students will learn about the science, practice, and social movement of agroecology through lectures, course discussions, field trips, and hands-on activities.

Population Genomics And Status Of The Flattened Musk Turtle (Sternotherus Depressus) In The Locust Fork Of The Black Warrior River, Seamus C. O'Brien

Theses

Alabama is home to some of the highest freshwater endemism in the world and ranks near the top in numbers of endangered and extinct species. One of these endangered species is the Flattened Musk Turtle (FMT), only found in the Black Warrior River Drainage of Alabama above the Fall Line. The FMT is listed as “Threatened” by the United State Fish and Wildlife Service under the Endangered Species Act and is considered Critically Endangered by the International Union for the Conservation of Nature due to drastic declines in populations since the 1980s. Declines have been attributed to several factors, including …

Hooks For Four-Dimensional Ecology Education (4dee) Teaching With Differing Audiences Of Nonmajors, Sara E. Scanga, Vikki L. Rodgers, Loren B. Byrne, Justin R. St. Juliana, Jon M. Honea, Erica S. Tietjen, George Middendorf

Arts & Sciences Faculty Publications

Nonmajors (i.e., undergraduate students not majoring in the natural sciences) constitute a majority of United States college graduates and are a large potential audience for courses with ecology content. However, nonmajors may be unmotivated to learn about ecology because they perceive it to be uninteresting and irrelevant to their everyday lives or career goals. Although the Four-Dimensional Ecology Education (4DEE) framework can be adapted for nonmajors courses as a starting point to improve student engagement, we suggest that nonmajors ecology instructors also use ecology hooks as effective gateways to 4DEE that will motivate and deepen student learning. Selecting and developing …

Cephalopod Consciousness: Asking The Right Questions, Gordon Burghardt

Animal Sentience

Jennifer Mather has provided a comprehensive and fascinating overview of the various cognitive accomplishments of cephalopods and their sensory, behavioral, and neurophysiological attributes. The advances in our understanding of a clade that has been separated from vertebrate evolution by well over half a billion years is a testament to advances in both methodology and the questions we now feel free to address. Mather embeds her review in the issue of consciousness, which is certainly a perennial issue in mental evolution, going back to Romanes and earlier. I argue that the term “consciousness” has such a checkered history and is used …

Antibiotic Resistance Trends In Coliform Bacteria Of Kittitas County Waters, Kaitlyn Holbrook, Bella Blasingim, Cruz Veronica Guillen Mejia, Holly Pinkart

Journal of the Symposium of University Research and Creative Expression

Project Mentor(s): Holly Pinkart, PhD

Since the mid-1900s, antibiotics have been developed to help fight against bacterial pathogens. However, bacteria can evolve rapidly and have evolved resistance to many types of antibiotics. Using coliform bacteria collected from waters around Kittitas County, BIOL 323 students at Central Washington University have identified a variety of antibiotic-resistant bacteria in Kittitas County streams and canals. Antibiotic resistance was measured from 2014-2019 and compared to data collected in 2024. This study focuses on three antibiotics, ampicillin, kanamycin, and trimethoprim-sulfamethoxazole. In the past (2014-2019) we saw no change in the trend of antibiotic resistance in collected …

Effect Of Coniferous Trees And Water Availability On Soil Acidification, Jessica A. Cheever

Journal of the Symposium of University Research and Creative Expression

Project Mentor(s): Mary Poulson, PhD

Water availability and coniferous tree species can cause acidification and a change in soil fertility. Previous research in European forests found that rainfall, soil acidity, and conifer prevalence influenced soil quality and biodiversity. However, not much is known about these effects in the Pacific Northwest’s forests. Three forests were chosen based on a gradient of annual precipitation. The Hoh Rain Forest, the Tiger Mountain State Forest, and the Okanogan-Wenatchee National Forest were used for wet, mesic, and dry conditions, respectively. Each location had a three-by-six grid spaced 50 meters between each plot. The location was …

Dynamics And Optimal Intervention Strategies In A Shigellosis Transmission Model, Mehmet Gümüs, Shewafera Wondimagegnhu Teklu, Kemal Türk

Mathematical Modelling and Numerical Simulation with Applications

This research explores how water treatment contributes to limiting the transmission of Shigellosis, an infection caused by bacteria from the Shigella genus. A mathematical framework is formulated to evaluate the influence of protective strategies and water purification on the spread of the disease. To confirm the model's biological relevance, its well-posedness is investigated. The basic reproduction number $(\mathfrak{R}_0)$, a critical indicator of disease behavior, is derived using the matrix operator method. Findings indicate that if $\mathfrak{R}_01$, the infection persists, with the endemic equilibrium exhibiting local asymptotic stability. A comprehensive cost-effectiveness analysis reveals that combining environmental protection with water treatment represents …

A Previously Unrecognized Species Of Celastrina From The Southeastern Coastal Plain Region Of The United States (Lycaenidae: Polyommatinae) Named In Honor Of The Memory Of Iryna Zarutska, Harry Pavulaan

The Taxonomic Report of the International Lepidoptera Survey

New species Celastrina iryna is described from the southeastern coastal plain of the United States. This species is most similar to C. neglecta but differs by possession of the unique dorsal overlay of clear wing scales found in C. ladon males. It is hypothesized that this may be a hybrid species. Some aspects of its life history remain unknown and call for further field research. The species name is a tribute to Iryna Zarutska, of Charlotte, North Carolina.