Life Sciences Commons^™

Systematics And Comparative Genomics Of The Petaluridae (Odonata: Anisoptera), Ethan R. Tolman

Dissertations, Theses, and Capstone Projects

The Anisoptera (Insecta: Odonata), or dragonflies exhibit diverse life histories and diversification patterns, with the family Petaluridae standing out as particularly unique. Comprising only 11 extant species, all of which inhabit increasingly threatened fen habitats, Petaluridae are known for their longevity, which can exceed five years, semi-terrestrial lifestyle, and remarkable physical size, ranking among the largest insects on Earth. Despite the evolutionary peculiarities of this family, no previous genomic studies have investigated the Petaluridae. This work presents two high-quality genome sequences and a targeted enrichment dataset to explore the chromosome architecture of Petaluridae, identifies genomic adaptations associated with their distinctive …

Metapopulation Genomics Of American Goshawks In The Intermountain West, Megan M. Sidran

All Graduate Theses and Dissertations, Fall 2023 to Present

Understanding a species dispersal ecology and population dynamics is essential to effectively manage and conserve a species. As advancing technology improves our knowledge of species movements, it is becoming clear that many species form metapopulations to some extent. A metapopulation is a network of interconnected subpopulations that exchange reproductive individuals with subpopulations occupying nearby patches. Metapopulations have been observed in a variety of species, ranging from plants to vertebrates, and can vary greatly in their dynamics (level of connectivity and gene flow) based on the species behavior and life history strategy.

Forming a metapopulation can add much resilience to the …

Genetic Evaluation Of The Current Distribution And Possible Diffrentations Between Lasiurus Borealis And Lasiurus Frantzii In Southwestern North America, Zeinab M. Haidar

Cal Poly Humboldt theses and projects

Several recent accounts of overlap and historic misidentifications regarding two species of the genus Lasiurus, Western red bat (Lasiurus frantzii) and Eastern red bat (Lasiurus borealis), have cast doubt on our understanding of their distribution, assumed spatial allopatry, and interactions in the United States Southwest. With the use of morphometrics and genetic sequencing, utilizing tissue collected from specimens throughout California and adjoining states, we have reassessed the current distribution, best practices for field identification, and genetic differentiation between both species. Appropriate species classification by region was achieved utilizing mitochondrial DNA, targeting the cytochrome c oxidase …

Effects Of Riverine Barriers On Avian Evolution In The Amazon Basin, Andre Eugene Moncrieff

LSU Doctoral Dissertations

The high biodiversity found in the Amazon Basin has long captivated the attention of naturalists and evolutionary biologists seeking to explain its origins. Early observations by Alfred Wallace highlighted the role of rivers in delimiting the geographic ranges of many species; furthermore, where rivers narrow towards their headwaters, he noted that some species cross rivers freely. A major goal of this dissertation is to investigate how these and other observations about riverine barriers might inform our understanding of how speciation unfolds in Amazonia. My approach involved generating genomic data with dense geographic sampling for manakins in the genus Lepidothrix, …

Riverscape Community Genomics Of Ozark Fishes: A Comparative Framework To Infer Ecological And Evolutionary Determinants Of Genetic Diversity, Zachery D. Zbinden

Graduate Theses and Dissertations

Genetic variation is a crucial component of biodiversity and represents the variability and spatial structure of alleles within and among organisms. Evolution modulates this variability over time through mutation, selection, gene flow, and genetic drift. However, our capacity to test foundational theories of population genetics has always been at the mercy of molecular approaches available to quantify patterns of genetic diversity. Initially, techniques for empirical DNA studies were in their infancy and limited by technologies and the price per unit of genetic information. Because of these constraints, our pursuits have generally been limited to investigations of one or a few …

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 …

The Influence Of Climate Change On The Ecology Of The Arctic Ground Squirrel In Denali National Park, Ak., Nigel A. Golden

Doctoral Dissertations

This dissertation research focuses on the ecology of the Arctic ground squirrel (Urocitellus parryii) in Denali National Park and Preserve, AK. The Arctic ground squirrels is a species of interest for monitoring efforts under the National Park Services’ Vital Signs Monitoring Program under the Vital Signs Monitoring program. The focus of this program is to monitor what is considered to be the most significant indicators of ecological conditions of the specific park resources that are of the greatest concern. The CAKN designated the Arctic ground squirrel (Urocitellus parryii) as one indicator species of park ecosystems. Despite being easy to observe …

Population Genomics Of Redbreast Sunfish (Lepomis Auritus): Exploring Gene Flow And Local Adaptation In A Widely Distributed Freshwater Fish, Garret J. Strickland

Electronic Theses and Dissertations

Little information is available concerning the distribution of genetic diversity in non-salmonid, non-imperiled, freshwater fish. In order to fill in this knowledge gap, I conducted a population genomics survey in Redbreast Sunfish (Lepomis auritus; RBS), a widespread, generalist species distributed along the Atlantic slope rivers of eastern North America. I sampled four basins (ACF, Savannah, Roanoke, and James) at eight sites each with a factorial experimental design. Sites were distributed among coastal plain, Piedmont, or mountain ecoregions in order to capture the greatest range of environmental states experienced by RBS, with the intention of finding evidence for local adaptation to …

Applying Conservation Genomic Techniques To Guide Management Of The Reticulated Flatwoods Salamander (Ambystoma Bishopi), Miranda Gaupp

Electronic Theses and Dissertations

The Reticulated flatwoods salamander (Ambystoma bishopi) is a federally endangered amphibian endemic to the longleaf-pine ecosystem of the southeastern U.S. This study used analyses of single-nucleotide polymorphism (SNP) data, collected from 2,255 unique individuals across 5 breeding seasons, spread across the known extant range of A. bishopi, to characterize the genetic diversity and demographics of populations, genetic relationships among populations, and patterns and spatial extents of gene flow, and to evaluate potential effects of management on A. bishopi’s resiliency. Population structure was strongly hierarchical, with individual breeding ponds (n = 38) acting as semi-connected subpopulations …

Quantifying Contributions Of Climate, Geography, And Gene Flow To Divergence: A Case Study For Three North American Pines, Constance E. Bolte

Theses and Dissertations

Long-lived species of trees, especially conifers, often display weak patterns of reproductive isolation, but clear patterns of local adaptation and phenotypic divergence. Discovering the evolutionary history of these patterns is paramount to a generalized understanding of speciation and the processes that confer population persistence versus those that compromise adaptive potential under rapidly changing environments. Forest trees have long generation times and low migratory potential making them especially vulnerable to population fragmentation and reductions of genetic diversity due to insufficient tracking of niche optima and adaptational lags. Within clades of the genus Pinus, evolutionary histories appear to be riddled with hybridization …

Landscape Population And Evolutionary Genomics Of Several Closely Related Species Of Mallard-Like Ducks, Joshua Brown

Open Access Theses & Dissertations

Divergence and speciation proceed through three major evolutionary forces (i.e., selection, genetic drift, and gene flow) that are often spatially and temporally heterogeneous across the landscape. Moreover, these forces can have differing but subtle effects within the genomes of diverging taxa, and therefore, disentangling the effects of these evolutionary mechanisms throughout the speciation process can be challenging. Here, I use a recent species radiation, the mallard complex, to investigate how strong, yet varied, evolutionary pressures influence the speciation process. The mallard complex consists of 14 mallard-like waterfowl species around the world that have some of the highest rates of hybridization …

Comparative Conservation Genomics Of A Suite Of Imperiled Freshwater Mussels, Scott C. Meyer

Electronic Theses and Dissertations

Maintenance of genetic diversity is a critical component to the management and recovery of imperiled species. By ensuring that a species’ genetic diversity is maintained, issues like inbreeding depression and loss of local adaptation can be prevented. However, the genetic diversity of many species are not well-characterized, and the factors that influence a species’ genetic diversity are often not well understood. In the case of imperiled unionid freshwater mussels, it is important to conduct conservation genetic assessments to aid in their management and preserve genetic diversity. This is the first study to conduct a comparative conservation genomic assessment for eight …

Evolution Of Green Blood In New Guinea Lizards: Phylogenomics, Biogeography, And Comparative Genomics, Zachary Rodriguez

LSU Doctoral Dissertations

Non-model organisms with evolutionary novelties and complex distributions can provide valuable insight into the mechanisms underlying biological diversity. Green blood is one of the most unusual vertebrate physiologies and has repeatedly evolved in lizards from the megadiverse island of New Guinea. An unusually high concentration of the toxic green bile pigment biliverdin causes the green coloration of these lizards' blood, muscles, and bones. This dissertation uncovered the complex history of this novel trait (Chapter 2), identified protein-coding sequences that underlie green blood in lizards (Chapter 3), and explored evolutionary processes that drive genetic diversity in high-elevation lizards. To accurately trace …

A Genomic Analysis Of Bobcat Populations In North America With A Comparison To The Canada Lynx: An Assessment Of Local Adaptation To Unique Ecoregions And Phylogeography, Jennifer C. Broderick

Electronic Theses and Dissertations

Bobcats (Lynx rufus) are an ecologically and genetically diverse species with a large contiguous range throughout North America. The species not only has a wide array of phenotypic variation compared to other mammals, but shows marked adaptability across ecozones with differing ecological influences. It is these various selective pressures in distinctive parts of the continent that have likely led to localized adaptations within the bobcat metapopulations. The species is also marked by its ability to maintain connectivity and populations in anthropogenically developed areas, an advantage it has over other felids, including its close relative the Canada lynx ( …

Mixing It Up: The Impact Of Episodic Introgression On The Evolution Of High-Latitude Mesocarnivores, Jocelyn P. Colella

Biology ETDs

At high latitudes, climatic oscillations have triggered repeated episodes of organismal divergence by geographically isolating populations. For terrestrial species, extended isolation in glacial refugia – ice-free regions that enable terrestrial species persistence through glacial maxima – is hypothesized to stimulate allopatric divergence. Alternatively, upon glacial recession, divergent populations expanded from independent glacial refugia and often contacted other diverging populations. In the absence of reproductive isolating mechanisms, this biogeographic process may trigger hybridization and ultimately, gene flow between divergent taxa. My dissertation research aims to understand how these episodic periods of isolation and contact have impacted the evolution of high latitude …

Genomics Based Approaches To Fungal Evolution, Aaron J. Robinson, Donald O. Natvig

Biology ETDs

Advances in DNA sequencing and data analysis make it possible to address questions in population genetics and evolution at the genomic level. Fungi are excellent subjects for such studies, because they are found in diverse environments, have short generation times, can be maintained in culture and have relatively small genomes. My research employed genetic approaches using a variety of sequencing technologies and methods of analysis to explore questions in fungal evolution.

In one study, I explored the genetics behind differences in thermotolerance between isolates of Neurospora discreta from Alaska and New Mexico. Isolates from the two states exhibited differences in …

Intraspecific Variation In Dehydration Tolerance: Insights From The Tropical Plant Marchantia Inflexa, Rose A. Marks

Theses and Dissertations--Biology

Plants are threatened by global change, increasing variability in weather patterns, and associated abiotic stress. Consequently, there is an urgent need to enhance our ability to predict plant community dynamics, shifts in species distributions, and physiological responses to environmental challenges. By building a fundamental understanding of plant stress tolerance, it may be possibly to protect the ecological services, economic industries, and communities that depend on plants. Dehydration tolerance (DhT) is an important mechanism of water stress tolerance with promising translational applications. Here, I take advantage natural variation in DhT to gain a deeper insight into this complex trait. In addition, …

Cisco Science: Using Omics To Answer A Range Of Key Questions, Hannah Lachance

Graduate College Dissertations and Theses

Coregonines, including cisco (Coregonus artedi), kiyi (Coregonus kiyi), and bloater (Coregonus hoyi), are a focus for prey fish conservation and restoration efforts throughout the Laurentian Great Lakes. However, fundamental questions about coregonine ecology and genetics remain. For example, we know little about how the early life stages of coregonines respond to environmental change at either the genotypic or phenotypic level. We also have limited knowledge about how to identify different species at the larval stage and the genetic relationships among species, which makes the different species difficult to study at the larval stage. To increase the probability for success in …

Population Structure And Connectivity Of A Groundwater Crustacean Across Northwestern Montana Aquifers, Megan N. Ritter

Master’s Theses

Floodplain aquifer systems are diverse and heterogenous ecosystems that serve many ecological functions, including habitat provision to a range of groundwater species. The Flathead River system of northwestern Montana is home to many floodplain aquifers of great ecological importance to the region. The basic biology, population structure, and dispersal patterns of obligate groundwater organisms that reside within the aquifers of the Flathead are still largely unknown. In this study, we investigate the population structure of one such taxon, an undescribed species of the amphipod genus Stygobromus. For our low-coverage RADseq dataset, we tested the suitability of three different analysis …

Grammar And Variation: Understanding How Cis-Regulatory Information Is Encoded In Mammalian Genomes, Dana Michele King

Arts & Sciences Electronic Theses and Dissertations

Understanding how genotype leads to phenotype is key to understand both the development and dysfunction of complex organisms. In the context of regulating the gene expression patterns that contribute to cell identity and function, the goal of my thesis research is to how changes in genome sequence may impact impact gene expression by determining how sequence features contribute to regulatory potential. To accomplish this goal, I first leveraged the key regulatory role of pluripotency transcription factors (TFs) in mouse embryonic stem cells (mESCs) and tested synthetically generated and genomic identified combinations of binding site for four TFs, OCT4, SOX2, KLF4, …

Evolutionary Dynamics Of Brown Treesnake (Boiga Irregularis) Reproductive Ecology, With Implications For Invasive Species Control, Brenna Aaren Levine

Graduate Theses and Dissertations

Invasive species represent major threats to biodiversity, global economies, and human health. Consequently, extensive research has been directed towards improving methods that restrict and contain them. Yet, control measures can also act as agents of selection by significantly impacting the reproductive capacity of invasives (in the context of “eco-evo” dynamics). The end result is that control measures subsequently alter the fitness landscape of an invasive over ecologically-relevant time, and lose their efficacy by so doing. However, adaptive management can be promoted by investigating the relationships between reproductive ecology, strength of selection, and (additive) genetic variation. In short, effective control can …

Speciation And Hybridization In Jamaican-Endemic Streamertail Hummingbirds (Trochilus Polytmus And T. Scitulus), Caroline D. Judy

LSU Doctoral Dissertations

Streamertails hummingbirds (Trochilus polytmus and T. scitulus) are recently diverged sister taxa that appear to have speciated in situ on the island of Jamaica. They are distinguished by male bill color, a secondary sexual trait that is coral red in T. polytmus and jet black in T. scitulus. They hybridize in a narrow zone where their ranges meet in eastern Jamaica. In Chapter 2, I performed a formal population survey of T. scitulus to determine the size of the population, which was unknown. I determined that the total population contains well over 100,000 individuals despite its limited …

Conservation And Variation Of Dna Methylation In Lactuca Sativa And Lactuca Serriola, Trudi A. Baker

Graduate Doctoral Dissertations

Molecular techniques for guiding plant breeding have successfully used wild progenitors of domestic crops as sources of genetic variants conveying desirable traits. However, epigenetic variation, in particular DNA methylation, is a significant source of phenotypic variation and epigenetic effects of plant domestication are poorly understood. Described herein are the first single-base pair resolution methylomes of the highly valued crop iceberg lettuce (Lactuca sativa cv. Salinas) and its close relative, and ubiquitous weed, L. serriola. This work suggests several roles for acquisition and inheritance of methylation in the evolution of Lactuca spp. in response to stress. The Lactuca spp. have conserved …

Assessment Of Genetic And Education Recovery Plan Objectives For The Bog Turtle (Glyptemys Muhlenbergii), Cassie Marie Dresser

Doctoral Dissertations

Unprecedented declines in biodiversity are threatening the natural world as we know it. Without human intervention, two thousand species listed under the US Endangered Species Act are likely to disappear. Fortunately, these species receive federal protection and increased research effort is needed to create and satisfy the objectives outlined in the mandated Species Recovery Plan. In this dissertation, I address three conservation objectives outlined in the Recovery Plan for North America’s smallest and rarest turtle, the Bog Turtle (Glyptemys muhlenbergii): (1) investigate the potential genetic differentiation in southern portions of the species’ range, (2) investigate the genetic impacts …

Systematics, Diversification, And Functional Diversity Of Russulaceae (Russulales), Brian Patrick Looney

Doctoral Dissertations

The family Russulaceae is an iconic family of mushroom-forming Basidiomycetes both because of their importance as edible mushrooms in many parts of the world and their species richness in both temperate and tropical forested biomes. While much mycological research has been focused on this group, recent systematic and ecological research has failed to develop a comprehensive or cohesive organization by which to understand the evolutionary relationships, patterns of diversification, or functional importance of the group. Recently, interest in ectomycorrhizal fungi (EmF), of which Russulaceae is a key lineage, has greatly increased due to the recognition of the importance of EmF …

Development Of An In Silico Kir Genotyping Algorithm And Its Application To Population And Cancer Immunogenetic Analyses, Howard Rosoff

Dissertations & Theses (Open Access)

Gene content determination and variant calling in the complex KIR genomic region are useful for immune system function analysis, pathogenesis and disease risk factor elucidation, immunotherapy development, evolutionary investigations, and human migration modeling. Sequence-specific oligonucleotide and sequence-specific primer PCR methods are the de facto standards for KIR presence/absence identification, but the current platforms are unsuitable for SNP calling, impractical for KIR typing large cohorts of DNA samples, and inapplicable for typing repositories in which sequence data, but not cells or cell analytes, are available. Alternative typing methods, such as in silico sequence-based typing, can address the problems associated with amplicon-based …

Physiology And Genetics Of Starvation-Selected Drosophila Melanogaster, Christopher Michael Hardy

UNLV Theses, Dissertations, Professional Papers, and Capstones

In nature, organisms have evolved to survive in stressful environments. This has driven organisms to adopt a wide range of unique adaptations. Investigating the mechanistic basis of these adaptations is an important tool for discovery that has led to major advances in science and medicine.

We study how organisms survive life without food, or starvational stress. Environmental stressors have shaped the quantity and quality of food sources across the globe. This has led to vast differences in the ability of some organisms to tolerate starvation over others. Many researchers have used Drosophila melanogaster as a model to study global patterns …