Ecology and Evolutionary Biology Commons^™

Dosage Sensitivity And The Evolution Of Dosage Compensation: Tests Of The Insensitive Sex Chromosome Hypothesis In Flour Beetles, Shana Pau

Biology Dissertations

Sex chromosome evolution generates imbalances in gene dosage that can disrupt gene expression and organismal function. These imbalances are often resolved through dosage compensation mechanisms, yet the factors that drive the emergence and diversity of these systems remain poorly understood. This dissertation addresses a central question in evolutionary genomics: what governs the evolution of dosage compensation?

Focusing on dosage sensitivity as a potential driver, I evaluate the Insensitive Sex Chromosome Hypothesis (ISCH), which predicts that chromosome-wide compensation is more likely to evolve in genomic contexts that are not depleted of dosage-sensitive genes. Using flour beetles (Tribolium spp.) as a …

Generating Genomic Resources For The Pink Sundew And Its Specialist Herbivore Moth From A Single Gene To Entire Genomes, Kerissa F. Tarpley

Honors Undergraduate Theses

Genomic resources are critical for the conservation of threatened species, providing valuable insights into genetic diversity, population structure, and adaptive potential. This thesis focuses on two ecologically interconnected species: the carnivorous plant pink sundew (Drosera capillaris) and its specialist herbivore the sundew plume moth (Buckleria parvulus). The sundew and plume moth face an uncertain future as their vital bog habitats continue to disappear. The sundew plays a crucial role in the life cycle of the plume moth, which relies on the sundew during its larval stages for survival. To aid in species detections, I first generated …

Analyzing The Loss Of Material From A Non-Plastic Oyster Reef Restoration Alternative, Lindsay M. Dolan

Honors Undergraduate Theses

Oyster reefs are declining globally due to human impacts such as overharvesting, boat wakes, and climate change. Associated ecosystem services, including water filtration, fish and invertebrates’ habitats, and shoreline erosion protection, are lost when these reefs disappear. Traditionally, restoration efforts employed plastic mesh shell bags filled with recycled oyster shells as they provide recruitment substrate for new oyster spat and wave attenuating properties to protect shorelines. Due to rising concerns over microplastic pollution, non-plastic alternatives are being tested. Alternative restoration material must provide the same benefits to reef formation while maintaining structural integrity long enough for a healthy reef to …

Adapting To Uncertainty: Effects Of Environmental Instability On Zebrafish Behaviour, Britney Sekulovski

Theses and Dissertations (Comprehensive)

This thesis addresses how animals cope with unpredictability by testing how environmental stability changes the behaviour of zebrafish (Danio rerio) in two complementary experiments. In Experiment 1, fish lived for three months in either a Dynamic environment (water temperature, feeding times, habitat complexity, group size, and membership fluctuated) or a Stable environment (all factors constant). Across seven behavioural assays, measuring individual behavioural differences, collective movement, social memory, and information use, Dynamic condition fish were found to be more sensitive to social cues and more likely to conform to recent social information, independent of the quality of the information …

Analysis Of Alternative Oxidase In Non-Angiosperm Plants, Anissa M. Francis

Theses and Dissertations (Comprehensive)

Alternative oxidase (AOX) is a mitochondrial terminal oxidase that provides an alternative pathway for electron transport, allowing plants to maintain respiratory flexibility under environmental stress conditions. While AOX has been extensively studied in angiosperms (flowering plants), little is known about its distribution and conservation in non-angiosperms. Based on gaps identified in the literature, this thesis investigated the distribution of AOX across non-angiosperm plant lineages. Although AOX is present in many green algae and is therefore considered to be an ancient protein that originated before the existence of non-angiosperm plants, it remains unclear whether the protein is uniformly distributed across these …

Evaluating Species At Risk In Data-Limited Fisheries: A Productivity-Susceptibility Analysis For Marine Aquarium Fish, Gabrielle A. Baillargeon, Alice A. Wynn, Jemelyn Grace P. Baldisimo, Michael F. Tlusty, Andrew L. Rhyne

Biological Sciences Faculty Publications

The marine aquarium trade (MAT) is a significant global industry harvesting millions of wild-caught, live coral reef fishes for public and private aquaria markets in the United States and Europe annually, while supporting fisher livelihoods in the Indo-Pacific. This diverse and species-rich trade is considered data-limited, creating barriers to quantifying the current and future socio-ecological sustainability of the fishery. We present a revised and expanded productivity–susceptibility analysis (PSA) that serves as a holistic risk assessment to estimate the vulnerability of marine aquarium fish to overfishing. Our global analysis includes 306 species that are actively in trade. Improvements to the PSA …

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 …

Viral Diversification And Host-Specific Fitness Of Powassan, Heartland, And Bourbon Viruses In New York State, Rachel E. Lange

Electronic Theses & Dissertations (2024 - present)

This dissertation reports important progress for our understanding of emerging and re-emerging tick-borne viruses circulating in North America including Powassan, Deer Tick, Heartland, and Bourbon viruses. Chapter 2 describes important tools for these viruses including multiplex assays for viral and bacterial pathogens in field-collected ticks and mammals, development of full genome sequencing assays and bioinformatic pipelines for evolutionary analysis, and establishment of tick-specific tools for viral isolation and characterization. Chapter 3 focuses on the disease focality of Deer Tick virus, reporting transovarial transmission in nature in Ixodes scapularis for the first time, further evidence to incriminate shrews as potential Deer …

Machine Learning-Based Spatio-Temporal Modeling Of Climate Dynamics And Desertification In The Sahara–Sahel Region, Stephen M. Tivenan

Theses and Dissertations

Arid climate classifications are threshold-dependent and easily interpretable mappings that are widely used in ecological, agricultural, and climate-related studies. These classifications inform scientific understanding, support policy and land management decisions, and provide an intuitive summary of environmental conditions. Despite their usefulness, traditional arid climate classifications often fail to quantify uncertainty, incorporate spatial context, or account for complex relationships among relevant environmental variables. Existing approaches to uncertainty assessment have largely relied on comparing classifications across multiple datasets or alternative formulas, but these methods generally overlook important spatial dependence and latent structure in the data.

This dissertation develops three machine learning-based statistical …

Climate, Biogeography, And Dispersal: A Unifying Framework For Ameri-Caribbean Dry Forests, Pablo Lopez Bustamante

Theses and Dissertations

Seed dispersal is a crucial ecological function that enables plants to alter their distributional range, avoid intense competition and natural enemies near the parent plant, and recover from disturbances. These processes shape species and functional composition of forests. Wind has traditionally been considered the dominant dispersal mechanism in Ameri-Caribbean dry forests, yet growing evidence suggests that other dispersal mechanisms also play significant roles in this ecosystem, responding differently to biotic and abiotic conditions. Still, how dispersal syndrome composition influences plant communities, the ecological drivers underlying these patterns, and the effects of climate change on dispersal syndrome dominance remain poorly understood. …

Compositional And Functional Shifts In Fish Community Structure In Response To Low-Head Dam Removals, Joshua D. Bruegge

Masters Theses

Low-head dams serve as intermittent barriers to aquatic connectivity and directly alter both upstream and downstream habitats and biotic communities. In 2018 and 2019, two low-head dams in the Vermilion River watershed of eastern Illinois were removed, reconnecting over 1,700 kilometers of upstream habitat within the basin. To determine the impacts of these dam removals, fish community surveys were conducted at 12 fixed sites across three reaches in two rivers from 2012-2022. This study assessed reach-specific temporal responses of the fish community and habitat characteristics. I linked trait expressions within the fish community to abiotic variables using the co-inertia RLQ …

Complexity Theory And Environmental Conservation Management: A Case Study With Coyote And Red Wolf Hybridization, Gretchen E. Mahalic

Honors Undergraduate Theses

Conservation biology and invasion biology are value-led scientific disciplines founded on environmental advocacy, operating at the intersection of research and action. Though these disciplines are known for their scientific veracity, unexamined values are often promulgated without scrutiny and drive decisions that work against good ecological outcomes. A case in point is that coyotes migrating into southeastern territory are framed as the greatest threat to the conservation of the endangered red wolf because hybridization is seen as diminishing their species integrity. Applying Val Plumwood’s ecofeminist account of dualistic frameworks, I will use this case to show how the vilification of the …

Sex In Plants: Birth, Death, And Trying To Survive In Changing Climates, Elena M. Meyer

Theses and Dissertations

Plant mating systems are key determinants of fitness. Angiosperms exhibit a wide variety of reproductive strategies, including self-fertilization (or selfing), outcrossing, and mixed mating. It has been estimated that up to 43% of plant species are capable of selfing, and selfing has been hypothesized to provide reproductive assurance where opportunities for mating may be limited, such as in marginal environments. However, questions regarding the overall distribution of selfing rates across angiosperms, the maintenance of mixed mating in the face of inbreeding depression, and the impact of self-fertilization on diversification rates remain incompletely resolved. Here, we explore the dynamics of self-fertilization …

Nutritional Niche Separation Amongst Sympatric Threatened Lemurs: The Role Of Micronutrients In Food Selection And Implications For Physiological Health, Maire K. O'Malley

Graduate Research Theses & Dissertations

Madagascar’s biodiversity is heavily affected by anthropogenic change and consequently, conservation management plans need to reflect current research to protect biodiversity. Primate nutritional ecology offers valuable insights into ecology, evolution, health, habitat requirements, social behavior, and conservation management strategies. Macronutrients (fat, carbohydrates, and protein) provide consumers with energy whereas micronutrients (vitamins and minerals) are essential to metabolic processes but are frequently overlooked. This study provides a novel examination of dietary niche separation by comparing mineral consumption between three sympatric species differing in feeding strategies: 1) Grey Bamboo lemur (Hapalemur griseus), a bamboo specialist, 2) Diadema sifaka (Propithecus diadema), a folivore, …

Layers Of Biodiversity: Linking Urban Garden Plants And Arthropods, Chenyang Su

Dartmouth College Ph.D Dissertations

Diverse arthropods play essential roles in urban agriculture, while urban agriculture provides food and habitat that support arthropod biodiversity in fragmented urban landscapes. In urban community gardens, a form of urban agriculture characterized by allotment-style gardens, arthropods interact with plants and green space across multiple spatial scales of management, from individual gardeners' plots to broad urban landscapes. Understanding how plant communities in urban community gardens and urban landscapes shape arthropod biodiversity and interactions across scales can inform both agricultural management and urban biodiversity conservation. In this thesis, I conducted a series of field studies on ecologically and economically important arthropods …

Evaluating Planting Methods For Native Seed Production And Exploring Granivory In The Northern Great Plains, Allison Dollen

Electronic Theses and Dissertations

Temperate grasslands have faced immense losses due to land use change in the last 150 years and less than half of the overall grasslands that once covered North America remain today. A portion of historic and remaining U.S. grasslands are located within the northern Great Plains (NGP) region which is home to over 1,600 species of native plants and provides many ecosystem services and economic benefits. Initiatives to restore grasslands and their ecosystem services are currently underway, but barriers such as limited native seed supply and granivory hinder restoration efforts. My first chapter addresses knowledge gaps in planting methods for …

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.

A Novel 3d Imaging Approach To Study Evolutionary Innovations In Solanaceae Inflorescences, Devin L. Jackson, Joonseog Kim, Wenheng Zhang Dr.

UROP Posters

Understanding the relatedness of angiosperms and the evolution of their inflorescence remains challenging, as these structures are highly modified and prone to convergent evolution. The current research describing inflorescence architecture, whether genetically or morphologically focused, typically relies on text based explanations, 2D images, or 3D based models created with CAD modeling software. This creates a disparity in the reader's understanding of these models since descriptions rely heavily on the author's interpretation of the inflorescence. The goal of our study is to bridge this disconnection by producing anatomically and color-correct 3D inflorescence models using Solanaceae flowers that readers can explore directly, …

Comparative Analysis Of Six New Chloroplast Genomes In Platanthera (Orchidaceae) Enhances Understanding Of Its Diversification, Lisa E. Wallace, Martin I. Batalla, Matthew Maisonave

Biological Sciences Faculty Publications

Platanthera is among the most diverse genera of orchids in north temperate regions, with high species diversity in Asia and North America. Despite many ecological studies in this group, little is known about its genomic diversity. Here, we report the newly annotated chloroplast genomes from six species in subgenus Limnorchis from North America and compare them with plastomes published for Platanthera species from Asia and Europe. We found that the plastomes of species in subg. Limnorchis are among the smallest reported for Platanthera thus far. While major structural differences were not detected in the newly sequenced species, ndh genes were …

From Theory To Ecosystems: Exploring Biodiversity And Ecosystem-Function In Pitcher Plant (Darlingtonia Californica) Microbial Communities, Gavin Sutter

Cal Poly Humboldt theses and projects

The relationship between biodiversity and ecosystem-function (BEF) has been a central focus of ecological research for the last three decades, yet the role of space in shaping BEF relationships remains relatively unknown. Research has shown that community diversity and composition can strongly influence productivity, nutrient cycling, and decomposition, but much of this work treats communities as spatially isolated, leaving open how dispersal and other spatial processes shape BEF at broader scales. To begin addressing this gap, I used microbial communities inhabiting Darlingtonia californica pitcher plant leaves to evaluate how spatial organization and successional change shape biodiversity and ecosystem-functioning. I quantified …

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.

Chesapeake Bay Water Clarity: Challenges And Successes, Jessica S. Turner, Carl T. Friedrichs, David B. Parrish, Kelsey A. Fall

OES Faculty Publications

The Chesapeake Bay is a large estuarine system spanning multiple jurisdictions and serves as a model for estuarine health worldwide. Historically, nutrient loading degraded water quality, prompting the need for regulation. Water clarity, one component of water quality, is vital for benthic communities and serves as a key indicator of overall ecosystem health. Here, physical resuspension and salinity gradients, nutrient and sediment inputs, production of organic detritus by phytoplankton, and benthic communities all interact to drive clarity patterns, with high spatial variability. Trends over the last 50 years show improvement, though with a temporary increase in organic detritus in response …

Microbial Mats In Dinosaur Ichnocoenoses, Nora Noffke, Paul C. Murphy, Roger C. Buntin, Martin G. Lockley

OES Faculty Publications

Until now, the significance of microbial mats in preservation of dinosaur tracks and in reconstructing the palaeoenvironment in which dinosaurs roamed was rarely studied. Dinosaur tracks are commonly found close to ancient aquatic bodies where moist sediment had once allowed footstep registration. At such sites, epibenthic or endobenthic microbial mats may have developed as well and may have led to exquisite track preservation. Microbial mats in coastal, lacustrine or flood plain environments cause 'microbially induced sedimentary structures—MISS', which are micobialites found in sandy or evaporitic settings. The microbial structures record environmental parameters including meteorological conditions that existed at the time …

Modeling Upper Ocean Ecosystem Dynamics In Response To Interannual Sea-Ice Variability In The Western Antarctic Peninsula, Catherine R. Czajka, Jessica S. Turner, Sharon Stammerjohn, Heather H. Kim, Oscar Schofield, Benjamin T. Saenz, Scott C. Doney

OES Faculty Publications

In the Western Antarctic Peninsula (WAP), marine plankton dynamics are tightly linked to the interannual variability in environmental conditions, including phenological shifts in sea-ice seasonality. To explore these linkages, we use a 1-dimensional vertical ocean-ice-ecosystem model (KPP-Eco-Ice, or KEI) that simulates physical and ecosystem conditions at a continental shelf mooring location in the Palmer Long Term Ecological Research program sampling grid. KEI allows for year-round examination of the ecosystem in a region where in situ observations on the shelf are limited to January. Comparisons are made between seasonal sea-ice retreat, mixed layer depth, primary productivity, and phytoplankton relative abundance, grazing, …

Aquatic Macrophytes As Nature-Based Solutions: Challenges And Opportunities Across Inland And Coastal Waters, Morgan Botrel, Roxane Maranger, Lindsay L. Trottier, Mathieu Cusson, Lars L. Iverson, Fanny Noisette, Christian Nozais, Katrine Turgeon, Andrea Bertolo, Thibaud André-Alphonse, Simon Bélanger, Arthur De Grandpré, Jean-Olivier Goyette, Sabine Hilt, Ladd Johnson, Valérie Langlois, Martin Laporte, Félix Lauzon, Brigitte Légaré, Anne Ola, Marie-Pomme Presne-Poissant, Matthieu Prugne, Caroline Susini, Richard Zimmerman

OES Faculty Publications

Macrophytes are foundation species whose use as nature-based solution (NbS) in aquatic ecosystems can help reduce climate change impacts while mitigating biodiversity loss. The discrepancy in research and application of macrophytes as NbS across inland and marine coastal ecosystems is an opportunity to expand the concept and learn from different approaches. We report on an initiative uniting marine and freshwater scientists that compared knowledge on macrophytes as NbS across realms, identified advances and gaps in their use, and synthesized challenges and opportunities for application. We conducted a bibliometric analysis and an expert participatory exercise around recent review papers. We reveal …

Microplastics Suppress Copepod Grazing Of The Harmful Algal Bloom-Forming Dinoflagellate, Alexandrium Catenella, Megan Ladds, Christopher Gobler

OES Faculty Publications

While harmful algal blooms (HABs) are prominent occurrences in coastal zones where microplastic concentrations are maximal, the manner in which microplastics may influence food webs and HABs is poorly understood. This study explored how polystyrene microplastics affected copepod grazing of the saxitoxin-synthesizing harmful dinoflagellate, Alexandrium catenella, as well as a non-toxic dinoflagellate, Gymnodinium aureolum. Experiments were performed using multiple densities of microplastics (250 – 10,000 mL^–¹) of differing sizes (4 and 10 µm), as well as multiple densities of microalgae in microplates. The addition of 10 µm microplastics at densities of 1000 – 10,000 beads mL^{– …}

Assessing The Diversity And Composition Of Crayfish Assemblages In The Ogeechee River Basin, Reginald Turner

College of Graduate Studies: Theses & Dissertations

Crayfish assemblage composition in the southeastern United States is understudied relative to other aquatic taxa, such as aquatic insects and fishes, and the Coastal Plain watersheds of that region are particularly underrepresented in the contemporary literature on this topic. For example, although 38% of the crayfish species in Georgia are considered “species of greatest conservation need,” most of the distributional data used to make these designations are outdated, with some dating back over 50 years. This thesis sought to update our understanding of the contemporary distributions of crayfish species within the Ogeechee River Basin (ORB), a watershed in southeastern Georgia …

Updates To Version 1.0 Of The Four‐Dimensional Ecology Education Framework Create Version 1.1., Christopher W. Beck, Loren B. Byrne, Jennifer Doherty, Amanda E. Sorensen, Et Al.

Arts & Sciences Faculty Publications

Since its introduction in 2018, the Four-Dimensional Ecology Education (4DEE) Framework has advanced ecology education. Yet, ecology educators have had different understandings of aspects of the Framework. Here, we describe the updates to the original Framework that aim to provide more clarity. Specifically, we describe higher-level changes in how the Framework is presented on the 4DEE website, changes to some of the elements within the dimensions, mostly in the Human–Environment Interactions dimension, and perhaps most substantively, replacing the lists of subelements with more descriptive paragraphs that explain the intent of the elements. We hope that these updates will promote the …