Life Sciences Commons^™

Dynamic Genomic Evolution Via Active Ltr Transposable Elements In Maize, Taylor Isles

Theses, Dissertations and Culminating Projects

Long terminal repeats (LTR) retrotransposons, found across eukaryotes, are transposable elements which can copy and insert themselves into other loci within a genome. These transposable elements are similar to retroviruses in that they rely on reverse transcriptase to “copy and paste” themselves elsewhere in the genome. From the RNA transcript they are able to use reverse transcriptase to make another DNA copy of themselves. This initially gave them the moniker, selfish genes. However, in the decades after the discovery of reverse transcriptase and LTR retrotransposons, it became known that non-genic DNA could have other functions. LTR retrotransposons are sources of …

Understanding The Environmental And Genetic Influence On Fluctuating Asymmetry And Developmental Instability In Primates, Ashly N. Romero

Graduate Theses and Dissertations

This dissertation explored the impact of environmental factors on the development and perpetuation of fluctuating asymmetry (FA) and sought to understand the role evolution may play in the FA exhibited in two primate populations: the free-ranging Cayo Santiago rhesus macaques (Macaca mulatta) and the Southwest National Primate Research Center olive baboons (Papio hamadryas anubis). Demographic, ontogenetic, secular, external, and genetic factors were examined. Specifically, this dissertation investigated FA over all ontogenetic stages, across decades, between sexes, in association with ecological catastrophes, and with tooth pathology to try and tease apart factors that may influence FA and developmental instability. This dissertation …

Host-Acquired Virus Genes Support An Ancient Antiviral Role Of The Pirna Pathway In Dipterans, Rebecca Christian

Theses and Dissertations

Endogenous viral elements (EVEs) have been recently investigated as a source of transgenerational immune memory. These “viral fossils” are abundant in Aedes mosquitoes and partner with the host’s primary antiviral defense system, the RNA interference (RNAi) pathways. This partnership appears unique to mosquitoes, which encode an expansion of the Piwi endoribonucleases. To interrogate EVE-Piwi partnerships and their role in antiviral defense, I performed a comparative small RNA analysis of two naturally occurring EVE-virus pairs – one in the mosquito Aedes albopictus, and one in the midge Chaoborus americanus. Both express an EVE related to the nucleoprotein of their …

Environmental Drivers Of Stress In Red Pandas (Ailurus Fulgens) : Behavior And Space Use Changes In Response To Redesigned Naturalistic Enclosures, Alexis Michelle Lawson

Theses, Dissertations and Culminating Projects

Animal welfare encompasses the physical and mental state of an animal, as well as how that animal is cared for. Recently, zoological settings have shifted from strictly housing animals to improving the welfare of the animal such that the goal of captivity is for residents to thrive. This is especially crucial as global wildlife numbers and biodiversity continues to decrease due to anthropogenic impacts such as poaching, mining, habitat destruction, fragmentation. Further confounding this issue is climate change, air pollution, invasive species, ocean acidification, and more. In particular, the red panda (Ailurus fulgens) is an endangered species whose declined 50% …

Vibroacoustic Response Of The Tympanic Membrane To Hyoid-Borne Sound Generated During Echolocation In Bats, Chelsie Snipes

Electronic Theses and Dissertations

The hyoid apparatus in laryngeally echolocating bats forms a mechanical connection between the larynx and auditory bullae and has been hypothesized to transfer the outgoing echolocation call to the middle ear during echolocation call emission. We used µCT data to build models of the hyoid apparatus and middle ear from six species of bats and used finite element modeling (FEM) to measure the vibroacoustic response of the tympanic membrane due to hyoid-borne sound generated during echolocation. We found that hyoid-borne sound in all six species stimulated the eardrum within a range likely heard by bats. Although there were minor differences …

Population Demography, Spatial Ecology, And Habitat Use Of The Florida Box Turtle (Terrapene Bauri) On A Barrier Island, Michael D. Mills

USF Tampa Graduate Theses and Dissertations

Turtles are one the most threatened vertebrate groups in the world due to anthropogenic threats such as habitat loss and overexploitation. In addition to occupying a range that has been vulnerable to major habitat loss, the Florida box turtle (Terrapene bauri) is particularly at risk of overexploitation due to its popularity in the pet trade. Sanibel Island is a barrier island in southwest Florida that has experienced major habitat loss and is the site of a recent poaching event. In response to these threats, studies of both the population demography and spatial ecology were conducted on Sanibel’s Florida box turtle …

Molecular Evolution And Biogeography Of The New World Eptesicus Bats, Xueling Yi

Theses and Dissertations

Molecular evolution refers to a broad field of studies ranging from microevolution (e.g., population genetics) to macroevolution (e.g., phylogeny), including the bridging field of phylogeography. In natural populations, molecular studies are also combined with biogeography that links biological diversity with geographic distributions to provide a comprehensive understanding of evolutionary processes. The field of molecular evolution has been largely advanced from early exploratory descriptions to statistical tests on biological hypotheses and integrative analyses using sophisticated modeling. However, studies of molecular evolution still face some unresolved questions and challenges, especially in non-model systems. For example, the application of new technology has largely …

Architecture Of Mate Choice Decisions In Enchenopa Treehoppers, Bretta Speck

Theses and Dissertations

Mate selection is one of the most important choices a female can make for herself and her offspring. Variation in mate choice decisions has consequences for the maintenance of and the diversity within a population and the promotion of divergence between populations. Mate choice decisions arise from the interaction of two main components: “mate preferences” (the relative attractiveness of a potential mate) and “choosiness” (the effort put into procuring a preferred mate). My dissertation analyzes the relationship between the components involved in female mate choice decisions in Enchenopa binotata treehoppers. I take a three-pronged approach. First, I investigated how E. …

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

University of New Orleans Theses and Dissertations

One of the most important gene families to play a role in adaptive immunity is the major histocompatibility complex (MHC). MHC class II loci are considered to be the most variable loci in the vertebrate genome, and studies have shown that this variability can be maintained through complex co-evolutionary dynamics between host and parasite. Despite the rich body of research into the MHC, there is comparatively little understanding of its genomic architecture in reptiles. Similarly, loci associated with innate immunity have received little attention in reptiles compared to other vertebrates. In the first chapter, we investigated the structure and organization …

Novel Method To Determine Paleodiet Of Extinct Equid Merychippus Sp. Using Dental Calculus, Ranjit Z. S. Virk

Senior Honors Projects, 2020-current

Within the Miocene Epoch, the emergence of grasslands within North America coincided with the incidence of higher-crowned teeth (hypsodonty) within the proto-horse Merychippus that allowed for the inclusion of these expanding grasslands as a food source. As herbivorous paleofauna consume plant matter, microscopic remains become incorporated within dental calculus and, due to their diagnostic morphology, can be used to identify dietary components. In Merychippus, the recovery of plant microfossils holds the potential to provide greater clarity on the paleodiet of these equids. In the present study, the purpose was to quantify and compare Merychippus paleodiet constituents among sample groups. …

Gut Microbiota Composition Is Correlated To Host Hummingbird Protein Requirements, Ryan C. Stanton , '20

Senior Theses, Projects, and Awards

The gut microbiome shapes and is shaped by a host animal’s physiology. Avian taxa hold physiological characteristics unique from mammals and might inform novel pressures experienced by microbial communities. Further, the symbionts’ relative abundance and their abilities to adapt to available resources are of critical importance to a holobiont’s fitness in rapidly changing climates. Therefore, wild populations of hummingbirds Selasphorus rufus and Calypte anna were studied. The two systems differ in S. rufus’s annual migrations from wintering grounds to their breeding grounds in the Pacific Northwest, whereas C. anna are resident in the latter region. Previous findings have indicated …

The Role Of Oxytocin On Social Behavior Associated With The Formation Of A Social Pair-Bond In The Socially Monogamous Convict Cichlid (Amatitlania Nigrofasciata), Christopher Garcia

Graduate Theses

The mechanisms for monogamy have evolved several times throughout history across various taxa in accordance with selective pressures. In vertebrates, monogamy is facilitated by the formation and the maintenance of social pair-bonds between mates. Social pair-bonds are a form of selective attachment that require complex neurobiological pathways in order to develop and continue. These neurobiological pathways are often regulated by neuroendocrine mechanisms, such as the release of the two neuroendocrine nonapeptides, oxytocin and arginine vasopressin, in specific parts of the brain or body. These neuroendocrine peptides play a big role in social and sexual behaviors. In prairie voles (Microtus ochrogaster) …

Analysis Of Baboon (Genus Papio) Population Structure Using Alu Insertion Polymorphisms, Corey St. Romain

Honors Theses

No abstract provided.

Phylogenomic Analyses Clarify Butterfly Species Within The Genus Speyeria Despite Evidence Of A Recent Adaptive Radiation, Erin Thompson

University of the Pacific Theses and Dissertations

The North American genus Speyeria is an especially challenging radiation of butterflies due to ongoing hybridization, incomplete lineage sorting, and similar morphological characters among species. Adaptive radiations often require considerable evidence in order to resolve the evolutionary relationships of closely related individuals. Previous studies of this genus have found paraphyly among species and have been unable to disentangle these taxa due to a lack of data and/or incomplete sampling of the genus. As a result, the interspecific relationships among Speyeria remain unresolved. In an attempt to achieve phylogenetic resolution of the genus, we conducted population genomic and phylogenomic analyses of …

Trypanosoma Cruzi Trypomastigote Glycosylphosphatidylinositol-Anchored Mucins And A Synthetic Alpha-Gal-Containing Neoglycoprotein As Potential Biomarkers And Vaccines For Chagas Disease, Igor Leandro Estevao

Open Access Theses & Dissertations

Chagas disease (CD), caused by the protozoan Trypanosoma cruzi, is a neglected tropical disease that kills or permanently disable thousands of people annually. About 6-8 million people are estimated to be infected worldwide. Although many efforts have been made for the development of an effective immunotherapy, currently there is no vaccine to prevent or treat CD in humans. Despite their toxicity, the two current drugs for CD, benznidazole (BZN) and nifurtimox (NFX), have medium-to-high efficacy in the chronic stage of the disease and could save or improve the lives of thousands of patients. However, negative seroconversion in treated patients, as …

A Bioinformatics Analysis Of Contributors To False Discovery For A Mouse Genotyping Array, Nisha Patel

Electronic Thesis and Dissertation Repository

Microarray experiments employing massively-parallel hybridization are valuable for the study of genetic variation, however, errors during hybridization and limitations of single-species design must be considered for use within and across species. The Mouse Diversity Genotyping Array (MDGA) is a low cost, high-resolution microarray with probes that bind to target DNA for variant detection. Errors associated with probe design and incomplete protein removal from target DNA lead to false discovery and thus necessitate examination of probe suitability and target DNA availability. Bioinformatics methods were used to carry out confirmation of probe annotations, assessment of DNA accessibility for hybridization to probes, and …

Investigations On The Role Of The Immune System In Mammary Development And Maternal Immunity In The Marsupial, Monodelphis Domestica, Bethaney Fehrenkamp

Biology ETDs

All newborn mammals are highly dependent upon milk for nourishment and immune protection. This is especially true for marsupials, a lineage of mammals with a short gestation, limited placental development, and an increased reliance on an extended lactation period. Most newborn marsupials do not receive passive maternal immunity in utero and therefore are entirely dependent upon factors within the milk for immune protection until capable of mounting their own response. In this project we seek to characterize the complex lactation program utilized by marsupials, and seek greater understanding of the maternal role in the establishment of the developing immune system …

Defining A Species: A Look At The Relationship Of Papio And Theropithecus Using Alu Elements, Paulina Gonzalez-Quiroga

Honors Theses

No abstract provided.

Sine Language: Communicating Platy-1 Retrotransposon Propagation In The Aotus Lineage, Jackson Mierl

Honors Theses

No abstract provided.

Whence And Whither: Acoustic Variability And Biogeography Of Tarsiers In North Sulawesi, Olivia Clare Kulander

Dissertations and Theses

The morning duet calls of eastern tarsiers (Tarsius spp.) in North Sulawesi were recorded and analyzed to examine the effects of geography and geologic history on their call structure. Tarsius species exhibit interspecifically variable duet calls shown to correlate with species differentiation and distribution. They are distributed across Sulawesi, a biogeographically complex island in the Indonesian archipelago, where tectonic activity and multiple glaciations during the Pleistocene generated and modified barriers to their dispersal and gene flow.

Recordings were made at ten locations from November of 2012 through June of 2014. Two locations were categorized as mainland, while eight island …

Evolutionary History Of The Mystr Retrotransposons And Connection To Myserv Elements, Tessa Passarelli

Senior Honors Theses and Projects

Retrotransposons are a group of transposable elements (TEs) that integrate into new chromosomal locations via an RNA intennediate. They are known as "jumping genes" and are transcribed as RNA, copied into DNA, and then moved to new sites in the genome. These elements comprise a large proportion of mammalian genomes. There are two types of retrotransposons- those with or without long terminal repeats. The most extensively studied family of L TR elements is known as endogenous retroviruses, which fonn when retroviruses integrate their own DNA within the genn line of their hosts. The mysTR family of LTRretrotransposons appears to be …

Biodiversity And Evolution In The Guiana Shield, South America, Andrew Michael Snyder

Electronic Theses and Dissertations

The neotropics are characterized as the most species rich region in the world. Unfortunately, the region's unparalleled biodiversity has not protected it from ongoing threats such as agriculture, mining, logging, oil extraction, and climate change. I studied the biodiversity and evolution of the herpetofauna of South America in order to investigate the influence of historical geological and climatological events in shaping extant neotropical diversity, particularly the Guiana shield. For my research, I set out to explore the processes involved in shaping the remarkable extant diversity using anuran amphibians as models. With my dissertation, I provide a comprehensive review of the …

Costs Of Group Locomotion: How Infant-Carrying And Group Members Mediate Walking Speed Decisions In North American And East African Populations, Leah M. Bouterse

Honors Projects

A major portion of humans’ activity-based energy expenditure is taken up by locomotion, particularly walking. Humans can offset the energetic expenditure of walking in numerous ways, both evolutionary (such as changes in body shape) and culturally. Behaviorally, people can choose to walk in a variety of ways, including alone or with a group, carrying loads, and walking quickly or more slowly. All of these behaviors have energetic outcomes and as such can be important windows into how populations and groups adjust to different constraints. While sex differences in speed of paired walkers have been established by others, the dynamics of …

Secrets Of Sines: The Story Of Platy-1 Propagation In The Saimiri Lineage, Sarah Brantley

Honors Theses

No abstract provided.

The Molecular And Cellular Basis For Cold Sensation, Daniel Brenner

Arts & Sciences Electronic Theses and Dissertations

The ability to sense changes in temperature is crucial to surviving harsh environments. Over the last decade several ion channels that have been proposed to be cold sensitive have been identified, most notably TRPM8 and TRPA1. Although these molecules have been extensively studied in vitro, their exact roles in cold sensation in vivo are still debated. This uncertainty is in large part due to problems with the standard methods of testing cold sensitivity in vivo, which often rely on subjective measures of cold responsiveness. Experiments using these subjective measures have been repeated by different groups and have yielded conflicting results, …

Analysis Of Western Lowland Gorilla (Gorilla Gorilla Gorilla) Specific Alu Repeats, Thomas Beckstrom

Honors Theses

No abstract provided.

Evolution Of Alu Element Subfamilies In Papio Baboons, Jon Hunter Strohmeyer

Honors Theses

No abstract provided.

Courtship Lateralization And Its Effect On Mating Success Of Male Wild Turkeys (Meleagris Gallopavo), Mara E. Vernier

Honors Theses

Lateralization results from unequal processing of tasks in the different hemispheres of the brain. While lateralization is a widely researched topic of study, little is known about the effects of sexual selection on lateralization. The purpose of this study was to determine if there is lateralization of male wild turkey (Meleagris gallopavo) courtship and whether the presence of lateralization is associated with male mating success. Male behavioral data were collected from video recordings of courtship made by Dr. Richard Buchholz during a previous mating study. Males were categorized as either successful or unsuccessful males based on how often they were …

Receptors For The Detection Of L-Amino Acids And Imp By Mouse Taste Sensory Cells, Shreoshi Pal Choudhuri

Graduate College Dissertations and Theses

The sense of taste is one of the most important factors in regulating ingestive decisions. This is central to a number of disease conditions including but not limited to obesity, diabetes, anorexia, hypertension, coronary artery diseases and malnutrition. The detection of the molecules eliciting taste qualities in food is mediated by the coordinated actions of distinct types of taste sensory cells (TSCs) housed in taste buds within specialized papillae throughout the oral cavity. Taste receptors in the taste sensory cells that detect food molecules are the key players in selecting dietary nutrients. One such example is L-amino acids, a critical …

Testing Visual Ecology Hypotheses In Avian Brood Parasite-Host Systems: The Role Of Uv-Light Perception And Egg-Nest Contrast In Foreign Egg Rejection, Zachary Aidala

Dissertations, Theses, and Capstone Projects

Color signals are highly important features of animal communication systems, particularly among birds, which possess exquisitely complex visual perception systems. Birds possess tetrachromatic vision, and some species are sensitive to ultraviolet (UV) wavelengths. Because human and avian visual systems dramatically differ (i.e. humans are not sensitive to UV wavelengths), biologically relevant sensory models are necessary to accurately assess the function of avian color signals. In this dissertation, I primarily use brood parasite-host interactions as a model for studying the behavioral function of avian-perceivable visual stimuli. In Chapter 1, I review the importance of employing biologically relevant sensory-perceptual visual models when …