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Theses/Dissertations

Life Sciences

Evolution

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The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson Mar 2024

The Evolution And Development Of Awns In The Grass Subfamily Pooideae, Erin L. Patterson

Doctoral Dissertations

This research focuses on a specific example of replicated evolution: the grass awn. Awns are typically extensions of the lemma, but may also appear on glumes or paleas. The lemma is a leaf-like organ on the exterior of the grass flower, the glumes are a pair of bracts subtending the basic unit of grass inflorescences, the spikelet, and the palea is the floral organ opposite the lemma. Awns are often described as "hair-" or "bristle-" like, but appear in many different shapes. Many awns are “twisted & geniculate", in which the awn has two sections, a lower twisted column, and …

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Evaluating The Effectiveness Of The Internal Transcribed Sequences (Its) As Dna Barcodes To Estimate Fungal Diversity, Jailisa Linares Dec 2023

Evaluating The Effectiveness Of The Internal Transcribed Sequences (Its) As Dna Barcodes To Estimate Fungal Diversity, Jailisa Linares

All HCAS Student Capstones, Theses, and Dissertations

Universal phylogenetic markers such as the nuclear ribosomal internal transcribed sequences (ITS), specifically ITS1 and ITS2, are routinely used to estimate fungal diversity in environmental samples. However, numerous studies report differences in the performance and efficacy of ITS1 and ITS2 in documenting fungal diversity. To better understand the implications of using ITS1 versus ITS2, a comprehensive representation of the diverse fungal taxa was necessary to conduct a meta-analysis of their use across multiple fungal taxa. In order to address this, a thorough literature review was conducted to compare and contrast the use of ITS1 and ITS2 as effective DNA barcodes. …

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Phylogeographic History Of The Leaf-Eared Mouse, Phyllotis Xanthopygus Complex, Tabitha R. Mcfarland Jul 2023

Phylogeographic History Of The Leaf-Eared Mouse, Phyllotis Xanthopygus Complex, Tabitha R. Mcfarland

Biology ETDs

Museum collections provide essential biodiversity sampling needed to understand the species limits, phylogeny, and biogeographic history of mammals, all key features of the foundation for comparative analyses in ecology and evolution. We add to this framework a diverse assemblage of species of leaf-eared mice (genus Phyllotis) in South America and then focus on the Phyllotis xanthopygus complex by combining available mitochondrial sequence (cytochrome b; cytb) data (351 GenBank samples) with 52 newly sequenced museum samples from the northern extent of this complex’s range (51 from Bolivia and 1 from northern Chile) to reconstruct evolutionary relationships using maximum …

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The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du Jul 2023

The Evolution Of Transposable Elements As Cis-Regulatory Elements In Mammals, Alan Y. Du

Arts & Sciences Electronic Theses and Dissertations

Transposable elements (TEs) are mobile genetic elements that make up a large proportion of mammalian genomes. Although TEs are highly prevalent genomic sequences, they have been understudied as they were once labeled as “junk DNA.” Despite their initial status as simple genomic parasites, recent studies have implicated TEs as cis-regulatory elements, supplying promoters, enhancers, and boundary elements. Functional testing of regulatory activity, however, remains a significant bottleneck. Nonetheless, due to their repetitive nature, TEs provide a unique model to examine the evolution of cis-regulatory elements, which has traditionally been difficult to study due to lack of homology at the sequence …

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Diversity, Function, And Phenotypic Plasticity Of Cryptophyte Phycobiliproteins, Kristiaän Merritt Jul 2023

Diversity, Function, And Phenotypic Plasticity Of Cryptophyte Phycobiliproteins, Kristiaän Merritt

Theses and Dissertations

Cryptophytes are a group of unicellular eukaryotic algae that can be found in a wide range of underwater habitats. Part of their ecological success can be attributed to their diverse array of cryptophyte phycobiliproteins (Cr-PBPs), a pigment class that captures wavelengths of light that are poorly absorbed by chlorophylls. Cryptophytes gained photosynthesis via secondary endosymbiosis in which their ancestor engulfed a red algal endosymbiont. Following endosymbiosis, they deconstructed the red algal photosynthetic machinery to form the Cr-PBP. Since then, the Cr-PBPs have diversified into at least 9 spectrally distinct forms. I investigated the diversity of Cr-PBP light absorption across 76 …

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Machine Kinship: The Impossible Duet, Diana Sanchez Jun 2023

Machine Kinship: The Impossible Duet, Diana Sanchez

Masters Theses

Machine Kinship: The impossible duet What does it mean to vanish from earth when you are the last of your kind? In 1987 the Kauai OO was recorded singing his final song. It was meant to be a duet, but as the last of his kind his song hangs in the air, unanswered. The other half of the duet is forever lost. Built to sing at dawn, birds must wake up earlier to hear each other before human chaos interferes. So here, it is always almost sunrise. As a parallel past-future response, the last birdsong was fed into a machine …

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Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata Jun 2023

Illuminating The Drivers Of Genomic Diversification In Lamprologine Cichlids Of The Lower Congo River, Naoko P. Kurata

Dissertations, Theses, and Capstone Projects

Freshwater fishes are extraordinarily diverse, considering their available habitats represent a tiny proportion of the earth’s surface. Rivers connect heterogeneous habitats in a linear form and provide excellent simplified models to understand how aquatic biodiversity evolves. In particular, the lower Congo River (LCR) in west Central Africa consists of a dynamic hydroscape exhibiting extraordinary aquatic biodiversity, endemicity, and morphological and ecological specialization. This system is thus an excellent natural laboratory for understanding complex speciation and population diversification processes. In my research, I explore various drivers of diversification, and adaptive evolution in rheophilic lamprologine cichlids endemic to the LCR, including Lamprologus …

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Impacts Of Bacterial Evolution On Host Lethality In Drosophila, Andrew Preston May 2023

Impacts Of Bacterial Evolution On Host Lethality In Drosophila, Andrew Preston

College of Arts & Sciences Senior Honors Theses

Evolution is the process by which species change their genetic traits, such as the pathogenicity of bacteria, over time in response to changes in their environment. Although the genetic mechanisms underlying many evolutionary processes have been revealed, it is still not well understood how opportunistic pathogens, such as Pseudomonas aeruginosa, become virulent. The overall goal of this thesis is to test the Coincidental Evolution Hypothesis, which proposes that the virulence of opportunistic pathogens evolves coincidentally as a by-product of their interaction with their natural predators. I hypothesized that the virulence of ancestral Pseudomonas aeruginosa changes over time if it co-evolves …

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Past And Present Patterns Of Neutral And Adaptive Genetic Diversity In Wild Mandrills (Mandrillus Sphinx), Anna Weber May 2023

Past And Present Patterns Of Neutral And Adaptive Genetic Diversity In Wild Mandrills (Mandrillus Sphinx), Anna Weber

University of New Orleans Theses and Dissertations

Although primates have fascinated researchers and the public alike for generations, one species that has remained enigmatic is the mandrill (Mandrillus sphinx), a large Cercopithecine monkey endemic to Central Africa. Mandrills are currently in decline due to bushmeat hunting, urbanization, and habitat loss. Neutral and adaptive genetic diversity are important tools for understanding evolutionary history and future viability, since diversity influences a species’ ability to adapt to a changing environment. However, thus far, minimal genetic information has been available for wild mandrills. Because of the dense vegetation in their tropical forest habitat, studying wild mandrills has proven to …

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Consequences Of Host Life Cycles For Symbiont Genome Evolution, Ashley Elizabeth Dederich May 2023

Consequences Of Host Life Cycles For Symbiont Genome Evolution, Ashley Elizabeth Dederich

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Aphids are small insects that feed exclusively on plant sap, a notoriously low source of nutrients due to the high sugar content and low amino acid content. To make up for these deficiencies in nutrition, aphids harbor Buchnera aphidicola, a bacterial endosymbiont that resides in a specialized organ called the bacteriome. B. aphidicola provides essential amino acids and vitamins for the aphid in exchange for a safe place to live. Over the course of the symbiosis (established 160 million years ago), B. aphidicola has lost much of its genome, including essential genes for cell envelope synthesis, DNA replication and …

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Context-Dependency And Sex-Specificity Of Dispersal Syndromes, Allyssa Kilanowski Jan 2023

Context-Dependency And Sex-Specificity Of Dispersal Syndromes, Allyssa Kilanowski

Theses and Dissertations--Biology

For populations in landscapes with increasingly heterogeneous and fragmented habitat patches (e.g., metapopulations), dispersal is an important behavior that leads to gene flow and connectivity among isolated patches. Because dispersal is a complex process, there are many traits involved. When suites of morphological, behavioral, physiological, and life-history traits covary with dispersal (e.g., a dispersal syndrome), the correlated traits can assist dispersing individuals through the complex process. Furthermore, once dispersal is completed, the correlated traits can influence the fitness of those dispersed individuals. Dispersal syndromes will likely interact with the local environment to produce ecological and evolutionary feedbacks on the metapopulation. …

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Investigating Plant Physiological Responses To Global Phylogenetic Diversity Of Glomeromycotina, David Z. Mowbray Jan 2023

Investigating Plant Physiological Responses To Global Phylogenetic Diversity Of Glomeromycotina, David Z. Mowbray

Honors Undergraduate Theses

Arbuscular mycorrhizal (AM) fungi are ubiquitous symbionts of terrestrial plant species with associations predominantly characterized as mutualistic. In addition to well-documented enhancement of host growth response, more recent analyses have demonstrated the conferral of host benefits under numerous biotic and abiotic stressors. However, much of the established evidence originates from studies involving limited AM fungal diversity. Accordingly, this study sought to evaluate the potential effects of inoculation on plant host physiological traits within a growth chamber environment, investigate potential correlations between host trait responses, & assess the degree of phylogenetic signal observed in trait responses due to the presence of …

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Effect Of Climate History On The Genetic Structure Of An Antarctic Soil Nematode, Abigail C. Jackson Dec 2022

Effect Of Climate History On The Genetic Structure Of An Antarctic Soil Nematode, Abigail C. Jackson

Theses and Dissertations

Historical climate disturbances such as glacial cycling and fluctuating stream, lake, and sea levels strongly influence the distribution and evolutionary trajectories of Antarctic terrestrial species. Antarctic invertebrates, with limited long-range mobility, including the ubiquitous sentinel nematode species Scottnema lindsayae, are especially sensitive to climate disturbances. We tested hypotheses associated with the historical geographic and population genetic structure of this species as it occurs across the McMurdo Dry Valleys (MDVs) of Antarctica. In order to reconstruct the influence of climate disturbance and ecological conditions on this species, partial mitochondrial COI gene sequences were sequenced and analyzed from individual S. lindsayae collected …

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The Development Of A Genomic Toolbox For Studying The Evolutionary Genetics Of Reptilian Lungs Using The Chicken Model, Logan Thomas Edvalson Nov 2022

The Development Of A Genomic Toolbox For Studying The Evolutionary Genetics Of Reptilian Lungs Using The Chicken Model, Logan Thomas Edvalson

Theses and Dissertations

There is a vast diversity in tetrapod lung branching morphology. Phylogenetically, much of the pulmonary diversity among vertebrates appears to arise from the way epithelial tubes branch or form saccular (cyst) structures. Fgf10 activity has been shown to play a critical role in regulating branch versus cyst morphology. We hypothesize that the species-specific differences in lung morphology may be primarily due to species-specific differences in Fgf10 expression. To test this hypothesis, we have performed bioinformatic analyses on the Fgf10 locus and have identified a conserved 11 kb noncoding region that potentially contains the Fgf10 lung enhancer. We are taking a …

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Ecology And Evolution Of Social Information Use, Clare T. M. Doherty Nov 2022

Ecology And Evolution Of Social Information Use, Clare T. M. Doherty

Dartmouth College Ph.D Dissertations

Sociality is a strategy many animals employ to cope with their environments, enabling them to survive and reproduce more successfully than would otherwise be possible. When navigating their environments and making decisions, social individuals often use information provided by conspecifics (in the form of social cues and signals), thereby increasing the scope and reliability of the information they can gather. However, social information use may be influenced by many factors, including key differences in context across the physical and social environment. My thesis asks and answers a series of questions regarding the trade-offs in social information use across different contexts, …

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Constraints Of The Imagination: How Phenotypes Are Shaped Through Genetics, The Environment, And Development, Michelle Gilbert Oct 2022

Constraints Of The Imagination: How Phenotypes Are Shaped Through Genetics, The Environment, And Development, Michelle Gilbert

Doctoral Dissertations

Phenotypic constraints are ubiquitous throughout nature, being found throughout all stages of life and at multiple different biological levels including cellular, genetic, environmental, behavioral, evolutionary, and developmental. These constraints have shaped, not only the natural world, but the way that we perceive what is possible, or impossible, an observation made clear by François Jacob in his 1977 paper “Evolution and Tinkering”. This is reflected in the literature, repeatedly, by the regular occurrence of densely packed visualization of phenotypic space that seemingly always have large areas that go unoccupied. Despite constrained regions of space being observable across countless taxa, identifying the …

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Ecology And Phytochemistry Of The Non-Native Plant Thlaspi Arvense (Brassicaceae) In Subalpine Meadows Of Colorado, Usa, Elsa Cousins Oct 2022

Ecology And Phytochemistry Of The Non-Native Plant Thlaspi Arvense (Brassicaceae) In Subalpine Meadows Of Colorado, Usa, Elsa Cousins

Doctoral Dissertations

Climate change is altering ecosystems at multiple scales. Globally, warming temperatures and increasing irregularity of precipitation will have large scale impacts on species distribution and success. Locally, understanding species response to fine scale microhabitat variation can provide key insights into population adaptation. Non-native plants represent an opportunity to investigate population level response and adaptation to relatively novel combinations of biotic and abiotic environments. Subalpine meadows are at the intersection of biotic and abiotic change, as large-scale climatic shifts alter water and temperature regimes and species range shifts become increasingly common and larger in scale. This dissertation addresses these questions of …

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Phylogenetic Relationships Among Fishes In The Order Zeiformes Based On Molecular Data From Three Mitochondrial Loci, Lindsay Scarpitta Oct 2022

Phylogenetic Relationships Among Fishes In The Order Zeiformes Based On Molecular Data From Three Mitochondrial Loci, Lindsay Scarpitta

Master's Theses

The Zeiformes (dories) are mid-water or deep (to 1000 m) marine acanthomorph fishes with a global, circumtropical, and circumtemperate distribution. Some species have a near-worldwide distribution, while others appear to be regional endemics, e.g., near New Zealand. Six families, 16 genera, and 33 species are currently recognized as valid. Relationships among them, however, remain unsettled, especially in light of recent proposals concerning the phylogenetic placement of zeiforms within the Paracanthopterygii rather than allied with beryciforms or percomorphs. The present study uses mtDNA characters to investigate zeiform interrelationships given their revised phylogenetic placement and attendant changes to their close outgroups, carried …

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Temperature Effects On The Development Of The Axial Skeleton And Body Shape In Astyanax Mexicanus (Teleostei: Characidae), Joseph David Forberg Aug 2022

Temperature Effects On The Development Of The Axial Skeleton And Body Shape In Astyanax Mexicanus (Teleostei: Characidae), Joseph David Forberg

College of Science and Health Theses and Dissertations

Humans are causing large-scale changes in environmental conditions across the planet including in temperature. Changes in the environmental conditions can lead to phenotypic changes in ectotherms that affect adaptively important traits like body shape and the axial skeleton. Previous studies have shown that temperature changes during development significantly affects body shape and vertebral number in the Mexican tetra Astyanax mexicanus. How these changes arise early in development is not clear. In this study, I examine how changes in developmental temperature affect body shape in larval and juvenile fish, the order of ossification of elements of the axial skeleton, the size …

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Acceptance Finds A Way: How To Teach And Use Evolution's Explanatory Power, Daniel George Ferguson Aug 2022

Acceptance Finds A Way: How To Teach And Use Evolution's Explanatory Power, Daniel George Ferguson

Theses and Dissertations

The theory of evolution is the central combing theory that brings together all the tenets of biology that bring about a solid understanding of life. It is also one of the most controversial scientific theories of all time and is widely rejected by about 40% of the general public in the United States. One of the biggest reasons for low evolution acceptance is the perceived conflict between evolution and religious beliefs. Educators and researchers have been working hard to improve how we teach evolution in the classroom; some methods, such as focusing on evolution knowledge, have shown to be mixed. …

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Development Of Graphical Models And Statistical Physics Motivated Approaches To Genomic Investigations, Yashwanth Lagisetty Aug 2022

Development Of Graphical Models And Statistical Physics Motivated Approaches To Genomic Investigations, Yashwanth Lagisetty

Dissertations & Theses (Open Access)

Identifying genes involved in disease pathology has been a goal of genomic research since the early days of the field. However, as technology improves and the body of research grows, we are faced with more questions than answers. Among these is the pressing matter of our incomplete understanding of the genetic underpinnings of complex diseases. Many hypotheses offer explanations as to why direct and independent analyses of variants, as done in genome-wide association studies (GWAS), may not fully elucidate disease genetics. These range from pointing out flaws in statistical testing to invoking the complex dynamics of epigenetic processes. In the …

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Mixed Method Analysis Of Undergraduate Student Interpretation Of Different Phylogenetic Trees, Faith Frings Jun 2022

Mixed Method Analysis Of Undergraduate Student Interpretation Of Different Phylogenetic Trees, Faith Frings

USF Tampa Graduate Theses and Dissertations

Phylogenetic trees are common tools used to visualize evolutionary concepts such as historical patterns of ancestry, divergence of species, and descent of species. However, students have misconceptions when reading these abstract diagrams. The purpose of this study was to compare student performance and evolutionary thinking when using two styles of phylogenetic trees: cladograms and phylograms. The study also assessed the validity of a hierarchal theoretical framework evaluating student phylogenetic tree interpretation. Introductory biology students from two research universities were assigned to two groups, one solely given assessments with phylograms, and one solely given assessments with cladograms. One-on-one student interviews were …

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Survivorship Of Columbian Black-Tailed Deer In A Predator-Free Environment, Grace Hope Barthelmess May 2022

Survivorship Of Columbian Black-Tailed Deer In A Predator-Free Environment, Grace Hope Barthelmess

Honors Projects

Future management of Columbian black tailed deer (Odocoileus hemionus columbianus) populations requires an understanding of survivorship and potential drivers of mortality. Little is currently known about the survivorship of O. h. columbianus, specifically in a predator-free environment. Analyzing the survivorship of deer in these contexts may be crucial for wildlife conservation efforts throughout the United States, as it could provide insight into how deer populations may be impacted by lack of population control by predation. Here, I present age analysis of O. h. columbianus based on the cementum annuli of the lower first molar in 489 males …

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Assessing The Utility Of The Pmm And Mmc Indices Among Extant Hominoid Genera, Julie A. Strain May 2022

Assessing The Utility Of The Pmm And Mmc Indices Among Extant Hominoid Genera, Julie A. Strain

Theses and Dissertations

This thesis set out to incorporate extant hominoid genera into an analysis of PMM and MMC to assess utility in phylogeny and predicting known taxonomic groups. Based on previous claims, we expect PMM/pmm and MMC/mmc to perform better than M1/m1 shape and size, our baseline for success, but they do not.

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Rodent Dental Microwear Texture Analysis As A Proxy For Fine-Scale Paleoenvironment Reconstruction, Jenny H. E. Burgman May 2022

Rodent Dental Microwear Texture Analysis As A Proxy For Fine-Scale Paleoenvironment Reconstruction, Jenny H. E. Burgman

Graduate Theses and Dissertations

Dental microwear texture analysis (DMTA) of fossil fauna has become a valuable tool for dietary inference and paleoenvironment reconstruction. Most of this work has utilized larger taxa with larger home ranges. These studies may result in broader-scale habitat inferences that could mask the details of complex mosaic habitats. Rodent DMTA offers an opportunity to work at finer spatial scales because most species have smaller home ranges. Rodents are also keystone species within their ecosystems, abundant, ubiquitous, and found in many fossil deposits. These attributes make them excellent proxies for environmental reconstructions. However, the application of DMTA to rodents remains relatively …

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Evolution Of Floral Microbes And The Resulting Effects On Pollinator Preference, Hailey Hatch May 2022

Evolution Of Floral Microbes And The Resulting Effects On Pollinator Preference, Hailey Hatch

Undergraduate Honors Capstone Projects

Floral microbes are an overlooked aspect of the extended floral phenotype. Through altering floral nectar chemistry, they can mediate interactions between flowers, pollinators, and other floral microbes, with significant implications for plant and pollinator health. Interactions between floral microbes and pollinators are critically important to understand, as pollinators provide important ecosystem services in both natural and agriculture systems. Here, I explored how floral nectar traits affected both evolution and competition within the floral yeast Metschnikowia reukaufii, the floral bacterium Bacillus subtilis, and other microbes isolated from Brassica rapa nectar, an important plant model system and oilseed crop. To …

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Comparative Sequence Analysis Elucidates The Evolutionary Patterns Of Yersinia Pestis In New Mexico Over Thirty-Two Years, M. Elizabeth Warren Apr 2022

Comparative Sequence Analysis Elucidates The Evolutionary Patterns Of Yersinia Pestis In New Mexico Over Thirty-Two Years, M. Elizabeth Warren

Theses and Dissertations

Yersinia pestis, a gram-negative bacterium, is the causative agent of plague. Y. pestis is a zoonotic pathogen that occasionally infects humans, and is endemic in the western United States. History gives evidence of three main plague pandemics. The first, originating in Egypt in 541AD, is known as the Justinian plague. The second, perhaps most well-known, is thought to have emerged in 1347AD in China, and is called the Black Death. The third, and current plague pandemic, also emerged in China in 1855. In 1899, Y. pestis was established in California, and the plague in other parts of America evolved from …

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Drought Tolerance In Native And Invasive Populations Of The Centaurea Jacea Hybrid Complex, Zoe Portlas Jan 2022

Drought Tolerance In Native And Invasive Populations Of The Centaurea Jacea Hybrid Complex, Zoe Portlas

Graduate College Dissertations and Theses

Introduced plants face many ecological and evolutionary challenges when establishing in a new range, such as strong abiotic stressors and potentially novel selective environments. One such abiotic stress is water availability, which is a strong selective force shaping physiological and phenological traits that enable plants to tolerate or avoid drought stress. Despite the challenges of establishing in a new range, thousands of species have become invasive in recent centuries. Two hypotheses that may explain how a species is able to withstand stress in its introduced range are preadaptation, which posits that species are adapted to similar environments in their native …

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Evolution Of Life-History Characteristics In Gadoidei, Joshua Hittie Jan 2022

Evolution Of Life-History Characteristics In Gadoidei, Joshua Hittie

Master's Theses

Life-history characteristics (e.g., age and growth) have been used extensively to understand the temporal population dynamics of fish species, but less so within a phylogenetic framework. This study investigates life-history characteristics within the suborder Gadoidei (order: Gadiformes) and to test the extent of phylogenetic signal for those characteristics. To accomplish this, a phylogeny of Gadoidei was first constructed based on both mitochondrial and nuclear genes. Within this phylogenetic framework, life-history traits, including growth rate, age at maturity, and longevity, as well as ecological data, such as water depth and diet type, were mapped to the phylogeny using parsimony analysis to …

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Geographic Range Size As A Predictor Of Dispersal-Dependent Behavioral Traits In Two Clades Of A Terrestrial Salamander, Teah Evers Jan 2022

Geographic Range Size As A Predictor Of Dispersal-Dependent Behavioral Traits In Two Clades Of A Terrestrial Salamander, Teah Evers

Masters Theses

Animal movement has the potential to affect diverse processes within ecology and evolution including range expansion, gene flow, adaptation, and speciation. Two aspects of animal personality that are germane to dispersal are exploratory and aggressive behavior. These behavioral categories may represent a trade-off such that energy invested in territorial defense leaves little energy for movement and dispersal. The Eastern Red-backed Salamander (Plethodon cinereus) is a wide ranging, dispersal limited, terrestrial salamander with well documented phylogeographic divisions. I examined dispersal-relevant behavioral traits within two clades of P. cinereus with disparate geographic ranges. The Northern Clade (NC) has a range extending from …

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