Genetics Commons^™

Genetic And Environmental Contributions To Wolbachia-Induced Cytoplasmic Incompatibility, Kelley Van Vaerenberghe

Graduate Student Theses, Dissertations, & Professional Papers

Maternally-transmitted Wolbachia infect the cells of most insect species, but their frequencies in host populations vary. While much of their success can be attributed to their ability to manipulate host reproduction, these manipulations are context-dependent, varying due to several biotic and abiotic factors. Wolbachia’s most common manipulation, cytoplasmic incompatibility (CI), is a conditional sterility phenotype where male-female host compatibility depends on their infection status. Specifically, CI occurs when infected males produce modified sperm that cause increased embryonic lethality unless the female carries a similar infection. Rescuing their eggs from CI increases the relative fitness of infected females, promoting Wolbachia spread …

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 …

Population Genomics Of The Giant Caribbean Sea Anemone Condylactis Gigantea (Anthozoa: Actiniidae) In Florida And Across The Caribbean, Nancy E. Sheridan

USF Tampa Graduate Theses and Dissertations

The giant Caribbean sea anemone Condylactis gigantea is a long-lived, conspicuous, and phenotypically diverse species native to the western Atlantic Ocean (from Bermuda to southeast Brazil), Caribbean Sea, and southeastern Gulf of Mexico. This sea anemone is an important benthic community member that provides habitat to numerous species, including cleaner shrimp. This relationship makes these animals desirable to aquarists for both enjoyment and the service provided by the shrimp for the overall health of an aquarium, and which is why they are sought.

The extraction of about 3.3 million C. gigantea individuals in Florida over a 23-year period for the …

Elevated Substitution Rates Among Wolbachia-Infected Mosquito Species Results In Apparent Phylogenetic Discordance., James E. Russell, Michael Saum, Rebekah Williams

Georgia Journal of Science

As one of the most widely distributed bacterial cytoplasmic symbionts on earth, Wolbachia pipientis Hertig serves as a model organism for the understanding of host-symbiont interactions. Many mosquito species are infected with Wolbachia strains that induce a form of reproductive manipulation called cytoplasmic incompatibility, in which infected females gain a reproductive advantage over uninfected females in mixed infection populations. The selective advantage of cytoplasmic incompatibility often results in a population sweep of Wolbachia and co-transmitted mitochondrial genomes. Mitochondrial evolution and phylogenetic inferences drawn from mitochondrial gene sequences are thus potentially compromised by reproductive manipulating symbionts, like Wolbachia. Our initial …

Investigation Of Dna Variability And Phylogenetic Relationships Of Perlesta (Plecoptera: Perlidae) In Mississippi, James C. Valentine, Mac H. Alford

Master's Theses

The genus Perlesta Banks, 1906 (Plecoptera: Perlidae) consists of 35 species, 33 native to the United States and Canada and two native to China. For over a century these small, brown stonefly adults and freckled yellow nymphs have gone by the name of the type species of the genus, Perlesta placida, but taxonomic work in the genus since 1989 has resulted in the recognition of additional species. These species were mostly recognized and described using morphological characteristics, but two areas that are lacking include (1) linking nymphs to adults and (2) phylogenetic analysis of all species occurring in Mississippi …

Cryptic Hybridization In The Temperate Bamboos: Is Pleioblastus Simonii A Species Of Hybrid Origin?, Morgan Brown

Theses

Japanese river bamboo (Pleioblastus simonii, ‘medake,’‘kawadake’) is an ecologically important species of temperate bamboo native to Japan. This species is widely known and historically important in Japanese rural farm life. Based on morphological data, Japanese river bamboo is classified in Pleioblastus section Medakea (Poaceae: Bambusoideae) along with five other Japanese species, which are collectively considered to represent a phylogenetically distinct lineage. However, recent studies suggest that Japanese river bamboo may have arisen as a result of previously undetected hybridization (i.e., cryptic hybridization), while also calling into question the diversity of section Medakea. The role of hybridization in natural plant populations …

Evaluating Population Genetic Structure And Potential Genomic Signals Of Natural Selection In A Migratory Songbird (Protonotaria Citrea), Tyler A. Hohenstein

Theses and Dissertations

In this study I attempted to further resolve the population genetic structure in the Prothonotary Warbler (Protonotaria citrea), and conducted an outlier SNP analysis and exploratory gene ontology analysis to investigate potential ongoing natural selection in the species. This analysis of population structure confirms previous work by DeSaix et al. (2019), where weak population structure was observed between eastern sites along the Atlantic Coastal Plain, and western sites in the Mississippi Alluvial Valley, possibly due to a genetic discontinuity across the Appalachian Mountains. I conducted two forms of outlier SNP analyses, a principal component analysis (PCA)-based approach to identify SNPs …

Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith

Graduate Theses, Dissertations, and Problem Reports (ETD)

Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …

An Analysis Of The Spatial Genetic Structure Of A Hybrid Zone Between Two Species Of Killifish, Fundulus Heteroclitus And F. Grandis, Andrew Lee Hardy

UNF Graduate Theses and Dissertations

Hybridization offers unique insight into the evolutionary process of speciation and the forces that maintain barriers to reproduction. In northeast Florida, a hybrid zone between two species of killifish, Fundulus heteroclitus and F. grandis, has been identified near Flagler Beach, FL, although the exact boundaries of the hybrid zone remain unknown (Gonzalez et al. 2009). This study aims to determine the fine-scale spatial genetic patterns of the hybrid zone and test the hypothesis that species ranges are influenced by changes in dominant vegetation. Results from an ADMIXTURE analysis and F_ST data indicated the boundary of the area of …

The Evolutionary Origins Of Autism Associated Genes And Their Role In Great Ape Socio-Communicative Behavior, Azeeza Abdulrauf

Master of Science in Integrative Biology Theses

Autism Spectrum Disorder (ASD) is a set of neurological disorders characterized by reduced social interactions and deficits in verbal and nonverbal communication. Although there are no clear genetic markers for ASD, studies have found associations between gene single nucleotide polymorphisms (SNPs) and patients diagnosed with ASD. For this study, the focus is on OXTR, AVPR1A, and FOXP2. OXTR is reported to regulate empathy and stress reactivity while AVPR1A is reported to regulate stress management and territorial aggression, as well as social bonding and recognition. FOXP2 is one of the first genes to be associated with both speech and language recognition …

Mitonuclear Mismatch Is Associated With Increased Male Frequency, Outcrossing, And Male Sperm Size In Experimentally-Evolved C. Elegans, Brent William Bever

Dissertations and Theses

We provide the first controlled study of how male frequencies and rates of outcrossing evolve in response to mitonuclear mismatch by allowing replicate lineages of C. elegans nematodes containing either mitochondrial or nuclear mutations of electron transport chain (ETC) genes to evolve under three sexual systems: facultatively outcrossing (wildtype), obligately selfing, and obligately outcrossing. In partial support of a tenet of the mitonuclear sex hypothesis, which predicts that outcrossing will be favored in cases of mitonuclear mismatch, we found evolution of increased male frequency in at least one replicate line of all four ETC mutant backgrounds tested--nuclear isp-1, mitochondrial …

A Reevaluation Of The Phylogeography Of The Chattahoochee Slimy Salamander (Plethodon Chattahoochee) Using Next-Generation Genomic Data, Jadin Cross

Symposium of Student Scholars

The Plethodon glutinosus species complex is a group of large-bodied, lungless salamanders that are widespread across the eastern United States. Species in this group are morphologically cryptic and were originally delimited using allozyme data, but in most cases, the extent of contemporary gene flow between named taxa has not be rigorously evaluated. The Appalachian Mountains of northern Georgia are home to several members of this group—including P. glutinosus, P. teyahalee, P. chlorobryonis, and P. chattahoochee. P. chattahoochee has been found to be especially cryptic both morphologically and genetically as both intraspecific genetic variation and species boundaries within …

The Evolutionary Origins Of Autism Associated Genes And Their Role In Great Ape Socio-Communication, Azeeza Abdulrauf, Martin Hudson, Susan M.E. Smith, Jared P. Taglialatela

Symposium of Student Scholars

Single nucleotide polymorphisms (SNPs) play a major role in socio-communicative behavior. For this study, the focus is on autism associated OXTR, AVPR1A, and FOXP2 SNPs, and the role they play in great apes. Prior research on the OXTR, AVPR1A, and FOXP2 SNPs show that they affect behavior skills such as understanding and controlling emotion, understanding the emotions of others, and communications skills. Great apes, such as bonobos, chimpanzees, and gorillas are the model, since they are our closest relatives in the animal kingdom capable of understanding complex communication. Each gene has at least two SNPS that are investigated in the …

Comparative Genomics Methods And Applications, Emily N. Alden

Biomedical Sciences ETDs

Virtually all fields of biology have benefited from the advancements in comparative genomics technologies, specifically in the study of evolution. In this dissertation I develop and use comparative genomic technologies to investigate the novel SARS-CoV-2 virus, assembly the first genome of the black lace domestic angelfish and identify germline genetic variants associated with altered breast cancer-specific survival. Our genome tiling array for the novel coronavirus presents a rapid and cost-effective method to sequence the entire viral genome and can be used to track the rapid evolution of viral variants in the population. The domestic angelfish is a member of the …

Dynamics Of Hybrid Zones At A Continental Scale, Bradley T. Martin

Graduate Theses and Dissertations

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional …

A Multispecies Perspective Into Dietary Genetic Adaptations And Ancient Migration In The Peruvian Andes, Kelsey Jorgensen

Wayne State University Dissertations

Successful adaptation to the high-elevation Andes would have required both cultural and biological adaptations by early human populations. These past adaptations continue to shape the evolutionary outcomes of both humans and non-human species today. A multispecies perspective was used to examine how humans and non-human creatures, specifically insects, were shaped by past human adaptations. This dissertation asked two primary questions: 1) Given the importance and evolutionary history of potato consumption in the Peruvian Andes, is a genetic adaptation to better digest potato starch detectable in present-day Peruvians? and 2) Using the Andean Potato Weevil (APW) phylogeny as a proxy, what …

Lepidopteran Granivory Reduces Seed Counts In A Rare Species Of Riparian Scour Prairies, Cheyenne Moore, Angela J. Mcdonnell, Scott Schuette, Christopher T. Martine

Faculty Journal Articles

In Pennsylvania Baptisia australis var. australis is found along only four waterways: the Allegheny River, Youghiogheny River, Clarion River, and Red Bank Creek. Because of its limited distribution and small number of extant populations, the species is considered state-threatened in Pennsylvania. In addition, the riparian prairie habitat that Pennsylvania Baptisia australis var. australis is restricted to is also in decline and considered vulnerable. Because of these conservation concerns, insights into the natural history of the taxon in the state is valuable and will inform conservation efforts. Field surveys and fruit collections along the Allegheny River and herbarium collections were used …

Breaking The Chain – The Role Of Intersexual Genetic Correlations In Sexual Dimorphism And The Consequences And Limits Of Their Evolution, Matthew Ma Maoloni, Tara Newman, Tristan Af Long Dr.

Theses and Dissertations (Comprehensive)

In many sexually reproducing species, males and females often differ in countless ways beyond their primary sexual organs. This phenomenon is known as sexual dimorphism, and it is generally considered to be an adaptive response to differences in the selection pressures experienced by males and females. Despite the advantages associated with sexual dimorphism, it does not evolve completely unhindered – there are plenty of biological effects that can limit the extent and rate of divergence between the sexes. This research project focusses on the potential role of the intersexual genetic correlation (r_mf­) – which describes the …

A Cophylogenetic Analysis Of Fungus Gardening Ants And Their Symbiotic Fungi, Katherine Beigel

Biology Theses

Fungus-growing ants (Tribe Attini) and their fungal cultivars share a 50-million-year coevolutionary history. Large scale phylogenetic analyses depict a strong co-phyletic signal among ants and their farmed fungi yet fungus sharing among unrelated ant lineages is somewhat widespread. An overview of sharing has been hampered by a lack of genetic markers that exhibit intraspecific variation and surveys across geographic regions. For example, previous studies have shown similar sequences of the internal transcribed spacer (ITS) region of fungus in different species of Trachymyrmex, suggesting that these ant species are farming the same fungal clone. To examine whether this was a …

Quantifying Structure And Variation In Complex Phylogenetic Data, Genevieve Geraldine Mount

LSU Doctoral Dissertations

Identifying the source and structure of variation in nature is crucial to understanding fundamental aspects of evolution. Despite a recent plethora of genetic and morphological data, many interesting questions about the relationships between different groups remain unresolved. My dissertation evaluates three approaches for identifying and quantifying the variation within phylogenetic datasets. Characterizing variation within datasets and across analytical methods gives insight into biologically interesting characters, unusual evolutionary processes, and areas for model improvement.

Network-based community detection approaches offer a powerful tool to describe variation in phylogenetic signal across the genome (i.e., gene tree variation). In Chapter 2, I investigate the …

Structure And Evolution Of Lizard Immunity Genes, Trent Santonastaso

LSU 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 …

The Evolution Of Bivalve Shell Matrix Proteins, Mark Ira Duhon Ii

LSU Doctoral Dissertations

This dissertation focuses on the molecular underpinnings surrounding the evolution of the biomineralized shells of marine bivalves. Bivalve molluscs synthesize remarkably complex shells from calcium carbonate and an organic matrix of proteins secreted from the dorsal edge of the mantle. Molecular analyses of shell matrix proteins (SMPs) have suggested high rates of gene turnover despite the conserved nature of the shell itself. Here, I used proteomic and transcriptomic data to identify the SMPs and other biomineralization proteins from seven bivalve species that diverged 3-513 Mya. Contrary to previous studies that identified only a few shared biomineralization transcripts across the Bivalvia, …

Evolutionary Inference From Admixed Genomes: Implications Of Hybridization For Biodiversity Dynamics And Conservation, Tyler Chafin

Graduate Theses and Dissertations

Hybridization as a macroevolutionary mechanism has been historically underappreciated among vertebrate biologists. Yet, the advent and subsequent proliferation of next-generation sequencing methods has increasingly shown hybridization to be a pervasive agent influencing evolution in many branches of the Tree of Life (to include ancestral hominids). Despite this, the dynamics of hybridization with regards to speciation and extinction remain poorly understood. To this end, I here examine the role of hybridization in the context of historical divergence and contemporary decline of several threatened and endangered North American taxa, with the goal to illuminate implications of hybridization for promoting—or impeding—population persistence in …

Evolutionary Ecology Of Host-Parasite Relationships: Role Of Host Ecology, Phylogeny, And Demographics In Shaping Parasite Evolution, Erika Taylor Gendron

Biology ETDs

Host-parasite systems exist across complex and ecologically heterogeneous landscapes, and may occur across taxonomically and ecologically disparate host species. Under these conditions, mechanisms underlying microevolutionary processes (i.e. gene flow, genetic drift) are not always clear, and may be mediated by numerous co-occurring factors specific to individual hosts. Host traits such as host immunology, demographics, phylogeny and ecology may act in concert to shape host-parasite relationships, and ultimately evolutionary processes. The research described herein used phylogeographic, phylogenomic, and population genetic methods to further understanding of how host traits impact the evolutionary ecology of trematode systems, using avian schistosomes (Digenea: Schistosomatidae) as …

Molecular Differentiation Of Astragalus Species And Varieties From The Western United States: The Chloroplast Dna Bridge Between Evolution And Molecular Systematics, Marwa Neyaz, Daniel Cook, Rebecca Creamer

Poisonous Plant Research (PPR)

Locoweeds are the most widespread poisonous plant problem in the world and have been reported in the Western United States since the 1800s, causing tremendous losses in livestock. Consumption of locoweeds by grazing animals stimulates the neurological disease, locoism, characterized by weight loss, ataxia, and lack of muscular coordination. The name locoweed is used for Astragalus and Oxytropis species known to contain swainsonine, the toxic principle produced by the plant endophytic fungus Undifilum. Astragalus includes 2,500-3,000 species and many varieties that have almost identical morphological characteristics that overlap among species, leading to improper identification. Therefore, the aim of this study …

On The Distribution Of Genetic Variation In Ecological Communities, Isaac Overcast

Dissertations, Theses, and Capstone Projects

Biodiversity in ecological communities is structured hierarchically across spatial and temporal scales. Many open questions remain as to how this structure accumulates. For example, what are the relative contributions of dispersal versus in situ speciation? Or, how important are stochastic drift versus deterministic processes? Up to this point, these questions have been investigated by isolated disciplines (e.g. macroecology, comparative phylogeography, macroevolution) using tools and data that tend to focus on only one axis of community scale data (e.g. phylogenies, relative abundances, and/or trait information). Yet we know that there are feedbacks among processes that respond on short, medium, and long …

The Origin And Evolution Of Flower Characters In Angiosperms With A Case Study On The Genetic Basis Of Zygomorphic Corolla Development In Bee And Hummingbird Pollinated Species Of Schizanthus (Solanaceae), Ghadeer Bukhari

Theses and Dissertations

This Ph.D. dissertation investigates two main projects separated into two chapters, one for each. The first chapter explores the evolution of flowering plants (angiosperms), a macro-scale study. The second project is on a micro-scale that focus on exploring the genes that regulate the similarities and the differences of flower morphology reflecting their different pollination syndromes in two species of Schizanthus (Solanaceae), i.e., S. pinnatus, a bee-pollinated flower, and S. grahamii, a hummingbird- pollinated flower.

In the first chapter, I used floral diagrams to study the origin and the evolution of floral traits in angiosperms, a new set of morphological data …

Spatial And Temporal Genetic Structure Of Winter-Run Steelhead (Oncorhynchus Mykiss) Returning To The Mad River, California, Steven R. Fong

Cal Poly Humboldt theses and projects

Distinct populations of steelhead in the wild are in decline. The propagation of steelhead in hatcheries has been used to boost population numbers for recreational fisheries and for use in conservation. However, hatchery breeding practices of steelhead can result in changes in genetic structure. I investigated the genetic structure of winter-run steelhead (Oncorhynchus mykiss) returning to the Mad River, California, where a hatchery has been used enhance production for recreational fisheries since 1971. Genetic variability in Mad River steelhead was evaluated using 96 single nucleotide polymorphisms (SNPs) among 4203 individuals, including the Mad River and nearby locations, and …

Developmental Mechanisms For The Diversification Of Polyphenic Morphs In The Head Horn Of Onthophagine Beetles (Coleoptera: Scarabaeidae Onthophagus Taurus): Plasticity Through Nutrition, Logan Paul Zeigler

Graduate Theses, Dissertations, and Problem Reports (ETD)

Developmental plasticity is the phenotypic variation between organisms that is caused by environmental interactions affecting the developmental systems of organisms. The research focused primarily on nutrition-responsive developmental plasticity. In this research we used the nutritionally determined head horn development of Onthophagus taurus to better understand the developmental mechanisms and genetic underpinnings of nutrition-responsive trait development. We focused specifically on altering the availability of specific nutrition-related primary metabolites, cholesterol and palmitic acid, identified in the activity of The Hedgehog pathway, a critical pathway in head horn development. By altering diet composition using cholesterol, reducing transcript expression of an acyltransferase gene, rasp …

The Host Gatekeeper: Using The Flagellar Pathway To Understand Symbiont Host Adaptation, Adam R. Pollio

Graduate Theses, Dissertations, and Problem Reports (ETD)

The acquisition of microbial partners is a strategy used by a diverse group of arthropods to overcome ecological barriers that might normally make certain niches uninhabitable. The unique phylogenetic opportunities attainable from the natural experiment of the Sodalis-allied clade allow for better understanding of how molecular structures evolve through time. Here, we focus on the evolution of the flagellar synthesis pathway, due to its complexity and ability to diverge in response to ecological pressures. We used this molecular pathway and natural experiment to show that normal evolutionary outcomes associated with symbiosis (i.e., genome reduction) do not explain the predicted conservation …