Ecology and Evolutionary Biology Commons^™

Exploring Factors Mediating White-Nose Syndrome In Little Brown Bats, Carly R. Trujillo

Graduate Theses/Dissertations

The little brown bat (Myotis lucifugus) has experienced drastic population declines across North America due to the recent disease white-nose syndrome (WNS). Previous studies have identified putatively adaptive alleles (PAAs) that may give individuals a greater likelihood of survival. However, there could be geographic-specific adaptation, creating different adaptive landscapes. Additionally, there may be energetic trade-offs between disease survival and reproductive output, and it is not clear what the long-term survival outcomes for the species may be as a result. Long-term evolutionary outcomes are unclear because this species has a lifespan exceeding the arrival of WNS and is difficult …

Impacts Of Native And Nonnative Plant Species On Avian Community Diversity, Matty John Mackay, Steven Van Dang, Brandon Lee Corn

SPARK Symposium Presentations

Avian communities play an essential role in maintaining a healthy ecosystem dynamic by regulating insect populations, assisting in plant pollination, and seed dispersal. These contribute to the overall health of natural ecosystems and mitigate ecological disruptions that would arise in their absence. However, the introduction of non-native invasive plant species can interrupt the balance avian communities bring to ecosystems by reducing availability of food sources, altering habitat structures, increasing competition among individuals, and disrupting ecological relationships through rapid invasion of ecological spaces. Point count observations of birds at Shelby Bottoms Park, Nashville, Tennessee in areas dominated by non-native privet and …

Hidden In The Mist: Three New Species Of Salamanders Of The Genus Pseudoeurycea (Amphibia: Plethodontidae) From Oaxaca, Mexico, Eduardo A. Aguilar-Herrera, Salomón Sanabria-Urbán, Dulce L. Flores-Martínez, José David Gómez-Tapia, Misael Seba-Chacha, Leopoldo D. Vázquez-Reyes, Francisco A. Rivera-Ortíz, Patricia Ramírez-Bastida, Bruno Cortés-Ortiz, R. Alejandro Calzada-Arciniega, Etienne U. Avila-Ortega, Dónovan I. Víquez-Vega, Omar Hernández-Ordoñez, Christopher Blair, Víctor H. Jiménez-Arcos

Publications and Research

We describe three new species of lungless salamanders (Plethodontidae) in the genus Pseudoeurycea from Cerro Rabon, located on the eastern slopes of the Sierra Mazateca, Oaxaca, Mexico. This mid-elevation mountain, largely surrounded by warmer lowlands, remains relatively understudied. We present molecular and morphological evidence distinguishing the three new species from their congeners. According to our phylogenetic analysis, one of the new species belongs to the P. leprosa group, while the other two are members of the P. juarezi group. Notably, one of the new species represents the fourth worm salamander known from west of the Isthmus of Tehuantepec, and another …

A Frog, A Toad, And A Salamander Walk Into A Forest: How Timber Harvest And Environmental Conditions Impact Amphibian Species Abundance In The White Mountain National Forest, William T. Brandenburg

Honors Theses and Capstones

Balancing the needs of humans and wildlife is one of the primary goals of conservation. Understanding how species respond to resource extraction is essential to achieve long-term population stability. This is especially relevant for amphibians, which are particularly sensitive to environmental disturbances due to habitat loss and degradation. As such they are often used as indicator species. This study leverages 20-years of amphibian abundance data from surveys in different silvicultural treatments to understand how American toads (Anaxyrus americanus), wood frogs (Lithobates sylvaticus), and red-backed salamanders (Plethodon cinereus) respond to changes in forest structure, weather, …

Current And Historical Occurrences Of Rare Coastal Plants In The Hampton Falls Salt Marshes, Liliana T. Chirichella

Honors Theses and Capstones

A botanical survey of two sites in the Hampton Falls saltmarshes was conducted to document the occurrences of a list of eleven endangered and threatened coastal plants listed in the Natural Heritage Bureau’s NH Rare Plant List. This survey was conducted in fulfillment of the NH Native Plant Protection Act to highlight and identify target species in an area where restorative runneling is to be implemented in order to restore proper hydrology and prevent further expansion of mega-pools in the Little River and Depot Road salt marsh sites, which have been subject to historical ditching and are a part of …

Fisheries Research Report No. 359: Metropolitan Monitoring Program 2025, Alissa Tate, Claire B. Smallwood, Karina L. Ryan, Troy Matthews

Fisheries Research Reports

Ongoing monitoring of recreational fisheries in the Perth Metropolitan zone is essential to ensure the sustainable use of fisheries resources. Surveys of shore- and boatbased recreational fishers within the Metropolitan zone of the West Coast bioregion provide information on human dimensions and catch-per-fisher as well as mean length and weight of key recreationally caught species. For shore-based fishers, estimates of fishing effort, catch and harvest are also presented for key nearshore species. This information is used to support ongoing assessments for key nearshore species and the development and evaluation of harvest strategies and other management actions, such as for Australian …

An Ecological-Evolutionary Investigation Of Phenotypic, Genetic, And Environmental Variation And Correlations Among Reproductive Traits Of Tall Goldenrod (Solidago Altissima), Michael J. Wise, Daniel Lavy, David E. Carr, Warren G. Abrahamson Ii

Faculty Journal Articles

Although fitness-related traits are expected to be under strong selection, traits related to reproduction are often quite variable within plant populations. We used data from two large greenhouse experiments to quantify phenotypic, genetic, and environmental variation, as well as genetic tradeoffs that might help explain the maintenance of withinpopulation variation in four traits related to sexual or vegetative reproduction in tall goldenrod (Solidago altissima). The goldenrod population exhibited high levels of both phenotypic and genetic variation for capitulum (flower head) number and size, seed production, and rhizome growth. Significant negative genetic correlations were present between the number of capitula and …

A Re-Evaluation Of Atlantic Bluefin Tuna (Thunnus Thynnus) Spawning Distribution In The Western Atlantic Ocean, David E. Richardson, Katrin E. Marancik, Malgorzata Adamus, Elizabeth A. Broughton, Robert K. Cowen, Trika Gerard, Christina M. Hernández, John J. Hoey, Joel K. Llopiz, Molly E. Lutcavage, Estrella Malca, Debra L. Palka, Lourdes Vásquez-Yeomans, Harvey J. Walsh, C. Michelle Willis, Glenn A. Zapfe

Biological Sciences Faculty Publications

There is currently a lack of consensus on the spatial, seasonal and decadal-scale patterns of Atlantic bluefin tuna (Thunnus thynnus) spawning in the western Atlantic Ocean. We compiled ichthyoplankton and reproductive data to characterize bluefin spawning patterns and the uncertainty in these patterns. Ichthyoplankton data indicates that bluefin spawn in the Gulf of America/Gulf of Mexico, northwest Caribbean Sea, north of the Bahamas, along the inshore edge of the Florida Current off the Carolinas and in the western Slope Sea. Reproductive studies identified these same spawning areas, as well as the Windward Passage and waters east of the …

False-Positive Detections In Avian Auditory Surveys: Effects Of Song Number And Directionality In A Calibration-Based Immersive Sound Environment, Katia Elena Chavez

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Detection-based surveys are widely conducted to monitor wildlife populations and provide data for estimating density and abundance. Avian count surveys are especially common because birds respond quickly to habitat degradation and restoration, making them effective indicator species. However, these detection-based surveys rely heavily on human observers and are prone to errors. If left unaddressed, these errors can bias estimates of species occurrence, and abundance, leading to misleading ecological inferences and management decisions. False-positive errors have received limited attention, in part because they are difficult to identify without independent confirmation of true species. To investigate false-positive rates in a controlled setting, …

Long-Term Banding And Encounter Patterns Of Cinnamon Teal Banded In Utah (1960-2025), Gracie A. Henrie

Undergraduate Theses, Professional Papers, and Capstone Artifacts

Utah is a valuable breeding and nesting ground for a number of waterfowl species, largely because of the Great Salt Lake, which supports over 400,000 acres of wetland habitat (Ducks Unlimited, n.d.). The Utah Division of Wildlife Resources manages 24 wildlife management areas (WMAs) with the purpose of creating high quality waterfowl habitat in these wetlands that can be enjoyed by hunters, recreators, and birds alike (Wildlife/Waterfowl Management Areas (WMAs), 2025). Effective management is supported with an understanding of the movement and demographic patterns of the waterfowl species the WMAs are designed to support. Bird banding is one tool managers …

Equid Major Histocompatibility Complex (Mhc) Evolution & Genome Organization, Lauren C. Johnson

Theses and Dissertations--Veterinary Science

The evolution of modern horses has a well-documented fossil record and has long been of interest to the genetics community. Although non-caballine equids (e.g. zebras, donkeys, and asses) can hybridize with horses, the resulting offspring are typically infertile. Despite these reproductive barriers, genomic analyses reveal regions of high sequence similarity among equid species. This dissertation investigates the role of historical introgression in the evolution of modern Equus species. The first chapter re-evaluates earlier findings derived from a limited horse population and a single reference genome. The variants of the identified regions were pushed through Ensembl’s Variant Effect Predictor to assess …

Using Camera-Based Unmarked Spatial Capture-Recapture Modeling To Estimate Reintroduced Elk (Cervus Canadensis) Population Parameters And Distribution In Southeastern Kentucky, Claire Marie Muia

Theses and Dissertations--Forestry and Natural Resources

Estimation of population parameters is important for wildlife management decisions. Elk reintroduced to southeastern Kentucky experienced early irruptive population growth and are currently monitored using a statewide harvest-based statistical population reconstruction model (SPR) across the Kentucky Elk Restoration Zone (KERZ). Because the SPR model is spatially coarse and difficult to scale to the smaller management units comprising the KERZ, we conducted a spatially explicit capture-recapture study using a clustered camera-trapping array deployed for 10 weeks from June–August 2024 to estimate elk population parameters within Management Unit 4. Due to a lack of resights of GPS-marked elk, population parameters were estimated …

Indirect Effects Of Coral Bleaching On Tursiops Truncatus Diet And Foraging Behavior In Bocas Del Toro, Panama, Annabel Fiero

Scripps Senior Theses

Indirect effects, where another species or factor mediates the effects of a given species, are critical to ecosystem structure and resilience. Shifts in fish community structure, as a result of rapidly declining coral reefs in the Caribbean due to warming-induced bleaching, pose a threat to apex predators like Tursiops truncatus (bottlenose dolphins). Branching corals create habitat niches for numerous fish species. These fish rely on coral for food and habitat, and in turn provide food for upper trophic levels. Prior research has highlighted how coral bleaching will disrupt Acroporid reef building corals and fish community structure, but the effects of …

Effectiveness Of Walleye Stocking In Winter Kill Lakes, Tyler Haus

Journal of Earth and Life Science

Winter kill events, marked by extensive fish mortality due to hypoxic conditions under the ice, are a common phenomenon in shallow eutrophic lakes, especially in the northern lakes in the northern United States. These events can drastically alter fish communities and often result in the elimination of top predators. Though these lakes will typically slowly bounce back to what they were in a couple of years. This study evaluates the effectiveness of walleye, Sander vitreus, stocking in lakes after a winter kill. For this study, four known winter kill lakes that are consistently stocked with walleye were studied. Pre- …

Size Structure Comparison Of Bluegill In Lakes With And Without Special Regulations, Jenna Lawin

Journal of Earth and Life Science

Lots of individuals have mixed feelings about special regulations for all sorts of game fish species such as northern pike Esox lucius, crappie Pomoxis spp., sunfish Lepomis spp., and so on. One species commonly sought after by many is bluegill Lepomis macrochirus. Bluegill are often deemed easy to find, catch, and clean. This study looks at three different categories of lakes (all lakes contain bluegill populations). The three categories are lakes with a five sunfish limit, lakes with a ten sunfish limit, and lakes without any special regulations. This study provides valuable insight into the size …

Western Massasauga (Sistrurus Tergeminus): A Species Conservation Assessment For The Nebraska Natural Legacy Project, Colleen Rothe-Groleau, Melissa J. Panella

Nebraska Game and Parks Commission: Publications

The Nebraska Natural Legacy Project recognizes the western massasauga (Sistrurus tergeminus) as a Tier I at-risk species. Provided are some general management recommendations regarding western massasaugas. Conservation practitioners will need to use professional judgment to make specific management decisions based on objectives, location, and a multitude of variables. This resource was designed to share available knowledge of this at-risk species that will aid in the decision-making process or in identifying research needs to benefit the species.

Criteria for selection as Tier I: State listed, G3

Estimated Population in NE: 1,000–2,500

Estimate based on: Field surveys

Trends since 2005 …

Population Dynamics And Future Viability Of The Eastern Massasauga Rattlesnake (Sistrurus Catenatus) In Southwest Michigan, Matthew John Klein

Graduate Theses, Dissertations, and Problem Reports (ETD)

Managing at-risk species or populations requires understanding the demographic and genetic drivers of long-term population trends. The eastern massasauga rattlesnake (Sistrurus catenatus) is a federally threatened species facing multiple interacting threats across its range. Habitat loss from wetland drainage and agricultural land conversion has caused range contractions and geographic isolation of populations. Because remaining populations are often small and widely separated, most are now genetically isolated, threatening their long-term viability. Reversing these declines requires understanding population dynamics, quantifying extinction risk, identifying drivers of long-term viability, and assessing the effects of inbreeding and the potential for genetic rescue to …

Survival, Cause-Specific Mortality, Resource Selection, Movement Rates, And Population Dynamics Of White-Tailed Deer (Odocoileus Virginianus) In West Virginia, Usa, Brett P. Skelly

Graduate Theses, Dissertations, and Problem Reports (ETD)

White-tailed deer (Odocoileus virginianus) are one of the most culturally and economically important big game species in the United States. At the turn of the 20th century white-tailed deer were almost extirpated due to market hunting and unsustainable forestry practices that destroyed habitat. The creation of game laws that eliminated market hunting and created seasons and bag limits for deer hunting along with restocking efforts by sportsmen’s groups and state wildlife agencies aided in deer population recovery. These efforts have led to the abundant deer populations that are currently enjoyed by hunters and wildlife viewers. Deer populations require …

Genomic Variation, Adaptive Evolution, And Invasive And Evolutionary History Of Microstegium Vimineum, Cameron William Corbett

Graduate Theses, Dissertations, and Problem Reports (ETD)

Invasive species can cause environmental and economic damage, but can offer unique opportunities to study rapid evolution and adaptation in novel environments. Microstegium vimineum (stiltgrass) is a prolific invasive grass in the eastern United States. Historical herbaria collections were used to identify patterns of invasion history and population dynamics over a spatial and temporal scale. Analyses of plastid genomes reveal a complex invasion history, including a single introduction in the southern United States linked to Japan and multiple repeated introductions in the northern United States from various source populations. Spread of introduced populations provide evidence of admixture among previously geographically …

Evaluation Of Brook Trout (Salvelinus Fontinalis) Thermal Tolerance And Projected Climate Change Effects On Headwater Brook Trout Population Persistence, Cory Bauerlien

Graduate Theses, Dissertations, and Problem Reports (ETD)

Climate change has been identified as one of the greatest threats to global biota in recorded human history. Consequences are expected to be more pronounced in ectotherms because most of their physiology is controlled by external temperature conditions. Predicting how ectotherms may respond to increasing global temperatures necessitates information about thermal limits of thermal sensitive species and how increasing temperatures may affect individual and population-level fitness. Therefore, the objectives of this research were aimed at gaining a better understanding of the mechanisms that underpin thermal tolerance limits of fish and how those mechanisms may affect fitness and population persistence under …

Using Side Looking Hydroacoustics And Community Size Spectra To Assess Invasive Carp’S Impact On Fish Assemblage Integrity, Daniel Jacob Bryan

Graduate Theses, Dissertations, and Problem Reports (ETD)

Often accounting for over half of total fish biomass, invasive silver carp have dramatically reshaped the ecosystem of the Mississippi River and its tributaries. These high silver carp densities have been shown to affect native fish body condition, abundance, and community structure, highlighting the need for efficient methods to quantify silver carp’s effect on the native fish assemblage. Community size spectra (CSS) is a metric that quantifies fish assemblage body size structure based on the decrease in fish abundance with increasing size. To estimate silver carp’s effects on CSS in the Ohio River, side looking hydroacoustic monitoring was used alongside …

Challenging And Diagnosing Structured Population Models By Testing Predictions From Stochastic Demography, Stephen P. Ellner, Robin E. Snyder, Daniel T. Blumstein, Dylan Z. Childs, Joshua C. Fowler, Christina M. Hernández, Julien G. A. Martin, María Paniw, Yngvild Vindenes

Biological Sciences Faculty Publications

1. Structured population models are parameterized to accurately project expected population sizes, stage/state distributions and population growth rates, but they also predict the variation in outcomes among individuals, such as the variance and skewness of lifetime reproductive output (LRO) and lifespan, the probability of never reproducing, and many other life-history metrics.

2. Testing such predictions about individual outcomes can be very useful model 'stress tests', because they depend on how components of the model (e.g. submodels for survival and fecundity) interact over multiple time steps, not just on the accuracy of the submodels. Because data on among-individual variation is rarely …

Hybridization And Introgression In Marine Invertebrates: Population Genomics Of Phymactis Papillosa And Asterias Sea Stars, Christopher J. Dookie

Dissertations and Theses

Hybridization and introgression are evolutionary significant processes in marine invertebrates (Sanford & Kelly,2011) yet genome-wide investigations of gene flow in these taxa remain limited relative to vertebrate systems (Marchi et al., 2021). This thesis presents genomic analyses of hybridization and introgression in two marine invertebrates occupying contrasting oceanographic settings and characterized by contrasting genomic datasets: restriction-site associated DNA sequencing (RADseq) SNP data for the eastern Pacific sea anemone Phymactis papillosa and whole genome sequencing (WGS) data for the North Atlantic sea stars Asterias rubens and Asterias forbesi. For each system, I applied coalescent-based species tree inference using CASTER (Zhang …

Non-Native Seagrass, Halophila Stipulacea, Reaches Northern Caribbean, Elizabeth R. Whitman, Elizabeth W. Stoner, Stephanie K. Archer

Gulf and Caribbean Research

Halophila stipulacea, a seagrass native to the western Indian Ocean, has become an established invader throughout the western Atlantic, where it often outcompetes native seagrass species across diverse environmental conditions. Here, we report its presence in the northern Bahamas, ca. 2300 km northwest of the first Caribbean record in Grenada and 304 km northeast of the recent observation in Florida, USA. This range expansion represents the northernmost Caribbean record to date and highlights the species’ capacity for long-distance dispersal and continued spread within the region. Our observation underscores the need for coordinated monitoring efforts to track the trajectory of …

Manatee Dock Sign Distribution And Its Influence On Publicly-Sourced Sighting Reports In Alabama, Daniela Payán Arias, Sophia C. Corde, Ruth H. Carmichael

Gulf and Caribbean Research

No abstract provided.

Geographic Distribution: Pseudacris Sierra (Sierran Treefrog). Usa: Florida: Escambia Co., Justin A. Anto, Logan P. Cutts, Jakira A. Davis, Dyrana N. Russell, Renee M. Shiska, Kayla L. O. Walker, Louis A. Somma

Papers in Herpetology

No abstract provided.

Geographic Variation In Proteomic Responses To Ocean Acidification In A Cold-Water Coral (Balanophyllia Elegans), Keana A. Richmond

Cal Poly Humboldt theses and projects

In the face of a rapidly changing climate, assessing organismal responses to future stressors in the context of current, natural exposure to stress could provide key insights to understanding marine ecosystem resilience. I used Balanophyllia elegans, a cold-water, solitary, azooxanthellate coral as a model to better understand how varying oceanographic conditions across its geographic range have shaped its ability to tolerate and potentially adapt to current and future ocean acidification conditions. I collected B. elegans individuals from four sites across 2,500km of their range and subjected them to two pH treatments to investigate site-specific protein expression in response to …

Larval Crowding In Culex Pipiens Generates Cumulative Cascading Effects Under Changing Environmental Conditions, Sengul Talay, Zafer Sakaci, Michele C. Weigle, Bugrahan Regaip Kilinc, Jenah Parman, Holly Gaff, Deniz Sirin, Bulent Alten, Dennis Bente, Sirri Kar

Computer Science Faculty Publications

Density-dependent population regulation is a fundamental driver in the population dynamics of living systems, ensuring a balanced and sustainable maintenance in nature. It has been suggested that the adverse developmental and morphological effect of high larval density in container mosquitoes represents a significant limiting factor for population density, and the need to investigate this possible importance within the framework of field-based principles has been emphasized. This semi-field study, conducted under the natural thermal regime and using a natural population in Turkish Thrace, aimed to examine the effects of non-food-limiting larval density (crowding effect) in the mosquito species, Culex pipiens ( …

Population Genomics And Evolution Of Pseudomonas Aeruginosa, Samara T. Choudhury

Electronic Theses & Dissertations (2024 - present)

Pseudomonas aeruginosa is a Gram-negative bacterium ubiquitous in diverse environments and an opportunistic pathogen in humans. It is a leading cause of chronic lung infections in cystic fibrosis patients and of hospital-acquired pneumonia and sepsis. With a large flexible genome and abundant mobile genetic elements, P. aeruginosa exhibits high levels of antimicrobial resistance (AMR), making it a significant public health threat. Evolutionary processes such as homologous recombination, and horizontal gene transfer generate extensive genomic diversity in this species and facilitate the spread of resistance genes. In this dissertation, I investigate the genetic and evolutionary factors shaping P. aeruginosa population structure …

Managing Multi-Drug Resistance: An Evolutionary Game Theory And Optimal Control Approach, Shukhrat Nasrulloev

Theses and Dissertations

Multi-drug resistance is an evolutionary process in which treatment eliminates sensitive cells, allowing resistant clones to dominate. This thesis investigates this process using a framework integrating population dynamics, evolutionary game theory, and optimal control theory. We develop a two-population logistic growth model describing competition between drug-sensitive and drug-resistant cells under treatment, construct dose-dependent payoff matrices and replicator dynamics to characterize evolutionary competition, and derive a critical drug level D_crit = (r_S - rR)/(dS - d_R) at which resistant cells gain a fitness advantage. An optimal control problem is formulated via Pontryagin's Maximum Principle to identify schedules …