Evolution Commons^™

Insights Into The Speciation Process From Genomic And Phenotypic Analysis Of An Avian Hybrid Zone In Amazonia, Glaucia Christina Del-Rio

LSU Doctoral Dissertations

Understanding the outcome of secondary contact is essential to shed light on the mechanisms governing species formation and maintenance. In Amazonia, closely related bird taxa with limited dispersal abilities are often separated by rivers, which presumably act as dispersal barriers. However, at the headwaters, rivers cease to be dispersal barriers, and this generates opportunities for secondary contact. In my dissertation, I studied genomic mechanisms associated with phenotypic differences, mitochondrial DNA structure, and putative reproductive barriers between two hybridizing Amazonian bird species in the genus Rhegmatorhina, a group of antbirds that find their arthropod prey exclusively by following army-ant swarms. …

Plastic And Evolved Responses In The Eastern Oyster, Crassostrea Virginica, To Environmental Variation In The Northern Gulf Of Mexico, Kyle Sirovy

LSU Doctoral Dissertations

Climate change and other anthropogenic impacts are causing rapid alterations to many of the world’s most productive coastal ecosystems and there is an urgent need to understand how species will respond to these environmental changes. Organisms may respond through plasticity, evolution, or the evolution of plasticity. In this dissertation, I evaluate the role of plastic and evolved responses in the eastern oyster, Crassostrea virginica, to environmental variation in the northern Gulf of Mexico. I use comparative transcriptomics, physiology, and morphology to examine the relative contribution of plastic and evolved responses for oysters exposed to low salinity and outplant sites …

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 …

Characterizing Endogenous Dicer Products To Unravel Novel Rnai Biogenesis Pathways, Jacob Oche Peter

Dissertations

ABSTRACT

RNA interference (RNAi) is a pervasive gene regulatory mechanism in eukaryotes based on the action of multiple classes of small RNA (sRNA). Exploiting RNAi pathways in non-model systems have great potential for creating potent RNAi technologies. Here, we accessed RNAi-mediated control of gene expression in the two-spotted spider mite, Tetranychus urticae (T. urticae) using engineered dsRNA designed to modulate the host RNAi pathway and increase RNAi efficacy. Analysis of Dicer (Dcr) generated fragments revealed how exogenous RNAs access the host RNAi pathway in this animal, opening avenues for designing RNAi technology for their control. Further, some organisms …

A Tale Of Two Genomes: The Complex Interplay Between The Mitochondrial And The Nuclear Genomes, Abhilesh S. Dhawanjewar

School of Biological Sciences: Dissertations, Theses, and Student Research

Mitochondria, the product of an ancient endosymbiotic event are pivotal to eukaryotic cells by synthesizing the majority of the cell’s ATP output. However, modern- day mitochondria are completely dependent on more than one thousand nuclear-encoded products for their function and the maintenance of their genomes. The fundamentally different ways in which the mitochondrial (mtDNA) and the nuclear (nucDNA) genomes are replicated and inherited lead to captivating coevolutionary dynamics between them. The aims of this dissertation are to investigate the coevolutionary dynamics between the mitochondrial and nuclear genomes at three distinct biological scales. At the organismal level, we use a Drosophila …

Genomic Insights Into Mechanisms Of Microbial Evolution And Evolution-Inspired Strategies To Combat Pathogen Diversity, Saymon Akther

Dissertations, Theses, and Capstone Projects

We live in an era of emerging infectious diseases that are increasingly common, rapidly spreading, and gravely devastating. Lyme disease, caused by bacteria belonging to the genus Borreliella, is rapidly rising in the Northern Hemisphere because of geographic range expansion of both the tick vectors and the pathogens. Evolutionary comparative analysis of Borreliella genomes is a key to understanding the phylogeographic history and mechanisms of their global diversification. Moreover, genomic variations in Borreliella associated with human pathogenicity, e.g., at loci encoding cell-surface antigens interacting with the vertebrate hosts, have not been fully identified. Similarly, the ongoing COVID-19 pandemic, caused …

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 …

Repeated Targets Of Natural Selection During Ecological Transitions Of Fish Across Salinity Boundaries, Jonathan P. Velotta, Stephen D. Mccormick, Andrew Whitehead, Catherine S. Durso, Eric T. Schultz

EEB Articles

Ecological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis …

Halodash: The Deep And Shallow History Of Aquatic Life's Passages Between Marine And Freshwater Habitats, Eric T. Schultz, Lisa Park Boush

EEB Articles

This series of papers highlights research into how biological exchanges between salty and freshwater habitats have transformed the biosphere. Life in the ocean and in freshwaters have long been intertwined; multiple major branches of the tree of life originated in the oceans and then adapted to and diversified in freshwaters. Similar exchanges continue to this day, including some species that continually migrate between marine and fresh waters. The series addresses key themes of transitions, transformations, and current threats with a series of questions: When did major colonizations of fresh waters happen? What physiographic changes facilitated transitions? What organismal characteristics facilitate …

Impact Of Genetic Variation And Timescale On Diatom Salinity Stress Response, Kala M. Downey

Graduate Theses and Dissertations

Natural environments are dynamic, and organisms must sense and respond to changing conditions. One common way organisms deal with stressful environments is through gene expression changes, allowing for stress acclimation and resistance which occurs over varying time spans in different species. The recent evolutionary history of populations could greatly influence their ability to respond successfully. An evolutionary history in disturbed or fluctuating conditions could promote increased resistance or a more rapid response to these environmental stressors. To understand the impact of genotypic variation and timescales on response and acclimation to salinity changes, we have been exploiting the abilities of euryhaline …

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 …

Phylogenomic Discordance Suggests Polytomies Along The Backbone Of The Large Genus Solanum, Edeline Gagnon, Rebeccca Hilgenhof, Andrés Orejuela, Angela J. Mcdonnell, Gaurav Sablok, Xavier Aubriot, Leandro Giacomin, Yuri Gouvêa, Thamyris Bragionis, João Renato Stehmann, Lynn Bohs, Steven Dodsworth, Christopher T. Martine, Péter Poczai, Sandra Knapp, Tiina Särkinen

Faculty Journal Articles

Premise of the study

Evolutionary studies require solid phylogenetic frameworks, but increased volumes of phylogenomic data have revealed incongruent topologies among gene trees in many organisms both between and within genomes. Some of these incongruences indicate polytomies that may remain impossible to resolve. Here we investigate the degree of gene-tree discordance in Solanum, one of the largest flowering plant genera that includes the cultivated potato, tomato, and eggplant, as well as 24 minor crop plants.

Methods

A densely sampled species-level phylogeny of Solanum is built using unpublished and publicly available Sanger sequences comprising 60% of all accepted species (742 spp.) …

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 …

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 …

Population Structure Of The Lizard Ecpleopus Gaudichaudii Coincides With A Biogeographic Barrier - The Doce River, Alexander J. Garretson

Dissertations and Theses

Intraspecific genetic variation is an integral component of diversification and the accumulation of biodiversity. The degree to which isolated populations of the same species are genetically structured in geographical space is impacted by a variety of mechanisms. In this study, I document patterns and discuss possible drivers of genetic structure within Ecpleopus gaudichaudii, a lizard species endemic to the Atlantic Forest of Brazil. For that, I assembled ddRadseq sequences from 48 individuals across much of the range of the E. gaudichaudii and analyzed its population structure. I created an intraspecific phylogeny for this group utilizing RAxML and conducted a …

Identifying The Human Homologs Of Yeast Rab Proteins Ypt10 & Ypt11 And A Global-Scale Louse Endosymbiont Genome Variation, Nathaniel P. Smith

Theses and Dissertations

Amyotrophic lateral sclerosis (ALS) is a late-onset fatal neurodegenerative disease that causes loss of upper and/or lower motor neurons, and currently has no treatment or cure available. Over 90% of cases occur spontaneously with unknown causes, highlighting the complexity of the disease, and only 10% of cases are linked to heritable genetic mutations. Numerous ALS-linked genes are conserved through evolution, and model organisms may therefore provide opportunities to understand disease pathology at a molecular or cellular level, proving instrumental in identifying therapeutic targets. ALS subtype 8 (ALS8) is caused by an autosomal dominant P56S mutation in the VAPB gene that …

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

College of Graduate Studies: Theses & 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 …

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 …

An Integrative Investigation Of The Synechococcus A/B Clade During Adaptive Radiation At The Upper Thermal Limit Of Phototrophy, Christopher L. Pierpont

Graduate Student Theses, Dissertations, & Professional Papers

Thermophilic microorganisms have been scientifically observed since the early nineteenth century and have spurred many questions about the limits of life and the capacity of organisms to survive extreme conditions. Decades of research on thermophile proteins and genomes have yielded several proposed correlates of temperature that may contribute to adaptation of bacteria and archaea to high temperature. However, many of the generalizations reported are drawn from analyses of deeply divergent taxa or from individual case studies in isolation from mesophilic relatives. Members of the Synechococcus A/B (SynAB) group are the only cyanobacteria with members able to grow above 65 °C …

Co-Option Of The Yolkless Oocyte Receptor For Crispr/Cas9 May Induce Transient Sterility In Female Drosophila Grimshawi Flies, Bronwyn Miller

LSU New Orleans Theses and Dissertations

Evolutionary developmental biology has historically used generalist model organisms like Drosophila melanogaster. The Hawaiian Drosophilidae radiation, which occurred just 25 million years ago, is an ideal lineage for work in Evo-Devo. Hawaiian flies make up 25% of the world’s Drosophila species and extreme diversity is seen throughout the group. D. grimshawi is a generalist Hawaiian picture-wing fly that has served as a model for the Hawaiian Drosophilidae radiation. However, D. grimshawi’s power and use as a model organism is constrained by our lack of ability to manipulate its genome. In this work, I attempted to edit the genome 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 …

Genetic Structuring And Community Assembly In Neotropical Birds, Oscar Johnson

LSU Doctoral Dissertations

The factors that influence how species form is of fundamental interest to biology. Under the framework of the speciation cycle, the process begins by population subdivision creating structured populations that then diverge until two new species form. Following speciation, however, continued divergence is necessary for these new species to be able to coexist without adverse interactions, known as the transition to secondary sympatry. At this point the speciation cycle is complete and the process can begin anew. Many of the factors influencing these processes remain poorly understood. Here, I explore the factors that influence speciation and community assembly in Neotropical …

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 …

Foe To Friend: Parallel Domestication Of Ophiocordyceps From Fungal Parasite To Beneficial Symbiont In Cicadas, Jason Vailionis, Eric Rl Gordon, Chris Simon

University Scholar Projects

Nutritional symbioses are integral to the survival and diversity of many insects. The majority of herbivorous insects in the order Hemiptera possess stable, inherited symbionts that produce essential amino acids and vitamins. However, instability has been observed in cicadas, with one bacterial symbiont, Hodgkinia cicadicola, being repeatedly replaced by a new fungal symbiont, Ophiocordyceps. The fungal symbionts are thought to be derived from parasitic Ophiocordyceps species, but little is known about these parasitic ancestors or how the transition from parasite to mutualist occurs. We used a combination of targeted amplified genes and metagenomic sequencing to investigate the evolution …

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 …

The Effects Of Climate And Demographic History In Shaping Genomic Variation Across Populations Of The Desert Horned Lizard (Phrynosoma Platyrhinos), Keaka Farleigh, Sarah A. Vladimirova, Christopher Blair, Jason T. Bracken, Nazila Koochekian, Drew R. Schield, Daren C. Card, Nicholas Finger, Jonathan Henault, Adam D. Leaché, Todd A. Castoe, Tereza Jezkova

Publications and Research

Species often experience spatial environmental heterogeneity across their range, and populations may exhibit signatures of adaptation to local environmental characteristics. Other population genetic processes, such as migration and genetic drift, can impede the effects of local adaptation. Genetic drift in particular can have a pronounced effect on population genetic structure during large-scale geographic expansions, where a series of founder effects leads to decreases in genetic variation in the direction of the expansion. Here, we explore the genetic diversity of a desert lizard that occupies a wide range of environmental conditions and that has experienced post-glacial expansion northwards along two colonization …

Diversity And Host Specificity Of Nycteribiid Bat Flies (Diptera: Nycteribiidae) In Kenya, Taylor Verrett

Masters Theses & Specialist Projects

Bat flies (Diptera: Nycteribiidae and Streblidae) are hematophagous ectoparasites of bats distributed globally. Members of Nycteribiidae are morphologically constrained relative to streblids, and are united by their lack of wings, dorso-ventrally compressed bodies, and a primary distribution across the Eastern hemisphere. Bats are principal reservoirs of infectious diseases, including viral zoonoses of important consideration to human health, but the overall high host specificity of bat flies has largely been thought to curb their potential as inter-specific vectors of bat-borne pathogens. However, nycteribiid diversity and host associations remain critically understudied in some geographic regions, and rare examples of nycteribiid bat flies …