Genetics and Genomics Commons^™

Species Delimitation Of Slimy Salamanders, Plethodon Kisatchie And Plethodon Mississippi, Across The Lower Mississippi River, Brock Hunter Stevenson

Master's Theses

Species are fundamental units of biodiversity yet delimiting species can be challenging. Slimy Salamanders of the Plethodon glutinosus species complex are a classic example of cryptic species for which species boundaries and relationships have proved difficult to determine. Once thought to be a single species ranging across the eastern United States, protein analysis revealed high genetic divergences among geographically distinct groups of populations, leading to 16 species being recognized within the group. Two of these species, the Louisiana Slimy Salamander (Plethodon kisatchie) and the Mississippi Slimy Salamander (Plethodon mississippi), are closely related but occur on opposite sides of the Mississippi …

A Case Of Incipient Budding Speciation In The California Floristic Province, Infraspecific Divergence In Abronia Villosa, Eli J. Allen

Cal Poly Humboldt theses and projects

Physical barriers to gene flow are the traditional evidence for species divergence. Conversely, there has been increasing acknowledgment of speciation in the face of gene flow as an evolutionary process. Budding speciation involves peripheral populations adapting to local ecological conditions, thereby budding off from a widespread progenitor species. Budding speciation is distinguished by ecological divergence and is generally evidenced by asymmetrical range size and nested phylogenetic relationships of sister species. The narrow endemic Abronia villosa var. aurita is adapted to montane sandy washes adjacent to its widespread sister variety, the desert dwelling var. villosa. Here, I tested the hypothesis …

The Genomic Dynamics Of Fermented Food Microbes, Katherine Chacón-Vargas

Doctoral Dissertations

Along with the agriculture and domestication revolution, humans have utilized bacteria, yeasts, and molds for millennia in the production of traditionally fermented foods and beverages. Fermentation is a very ancient practice of high relevance nowadays since it contributes with a great variety of foods worldwide. Microbial fermentation allows metabolic transformation of the raw food materials leading to biochemical changes that played a key role in food preservation, health benefits, nutrition, flavors, and texture, among others. Food fermentation practices could diverge from traditional artisanal spontaneous fermentation to industrialize methods with specialized microbial starters and although fermented environments tend to be very …

Placing The Evolutionary History Of Desmognathus Salamanders In Context: A Phylogeographic Approach, Kara Jones

Theses and Dissertations--Biology

Patterns of genetic variation do not arise in a vacuum but are instead shaped by the interplay between evolutionary forces and ecological constraints. Here, I use a phylogeographic approach to examine the role that ecology played in lineage divergence in the Desmognathus quadramaculatus species complex (Family: Plethodontidae), which consists of three nominal species: D. quadramaculatus, D. marmoratus, and D. folkertsi. Previous phylogenetic studies have shown that individuals from these species do not form clades based on phenotype. My approach to reconciling phylogenetic discordance was two-fold, using (1) genome-wide markers to provide insight into 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 …

A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens

Dissertations

Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …

Reassessment Of Species Boundaries And Phylogenetic Relationships In The Desmodium Ciliare Complex (Fabaceae) Using Morphological And Dna Data, Joshua Wilkinson

Master's Theses

Desmodium (Beggar's ticks) is a generally weedy genus of approximately 280 species in the angiosperm family Fabaceae (Subfamily Papilionoideae, Tribe Desmodieae) characterized by indehiscent loments constricted into segments. Within the Southeastern U.S., the Desmodium ciliare group is one of two Desmodium species complexes that have been historically difficult, with much argument about the limits of species and the role of hybridization. There are three commonly recognized species within the D. ciliare group, D. ciliare (Muhl. ex Willd.) DC., Desmodium marilandicum (L.) DC., and D. obtusum (Muhl. ex Willd.) DC., with two supposed hybrids in addition to the …

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 …

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 …

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 …

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 …

Taxonomy And Systematics Of Plumeria L. (Apocynaceae) In The Caribbean Islands, Nichole M. Tiernan

FIU Electronic Theses and Dissertations

Plumeria L. (Apocynaceae) is a genus of flowering trees and shrubs that are often cultivated in tropical gardens worldwide. The majority of its species occur in the Greater Antilles with many as single-island endemics. The only comprehensive revision for the genus was done by Robert E. Woodson Jr. (1937) who recognized only seven species and created a ‘Plumeria obtusa complex’ with a plethora of synonyms. The first study provides an overview of the Caribbean Island members of the genus with a focus on Plumeria filifolia Griseb., a thin-leaved species endemic to Cuba that is featured because of its incredible …

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 …

Identification And Sequence Analysis Of Set Superfamily Genes In Hymenopteran Insects, Tanima Joshi

Scripps Senior Theses

Post-translational chemical modifications of histones, the proteins that package DNA, are a key component of the “language” of epigenetics. SET (Suppressor of Variegation 39, Enhancer of Zeste, Trithorax) domain-containing proteins are crucial enzymes that establish histone methylations as a major part of the histone code. Studies using the fruit fly, Drosophila melanogaster, as a model organism have provided most of the known information on SET genes/protein diversity and function in insects. To expand our knowledge of this important protein family, I identified all SET domain-containing genes in a select group of insects belonging to the Hymenoptera order: wasps, bees, ants, …

Genome-Wide Characterization Of Lateral Organ Boundaries Domain Genes In Sunflower (Helianthus Annuus L.), Saleh M. Aljurbua

Masters Theses

Lateral Organ Boundaries (LBD) gene family encodes transcription factors found only in plants with essential roles in growth, development, and response to biotic and abiotic factors. The sunflower (Helianthus annuus L., Asteraceae family) LBD genes were studied using different in silico and phylogenetic approaches including four major steps: gene identification, phylogenic analysis, structural analysis, and expression analysis. Sixty-four sunflower LBD genes (HaLBDs) were identified using query search of all Arabidopsis LBD genes against sunflower genome (version r1.2) followed by LBD domain sequence verification. A phylogenetic tree was reconstructed using MEGA-X program. The identified genes were phylogenetically classified into two main …

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 …

Rates And Patterns Of Indels In Hiv-1 Gp120 Within And Among Hosts, John Lawrence Palmer

Electronic Thesis and Dissertation Repository

Insertions and deletions (indels) in the HIV-1 gp120 variable loops modulate sensitivity to neutralizing antibodies and are therefore implicated in HIV-1 immune escape. However, the rates and characteristics of variable loop indels have not been investigated within hosts. Here, I report a within-host phylogenetic analysis of gp120 variable loop indels, with mentions to my preceding study on these indels among hosts.

We processed longitudinally-sampled gp120 sequences collected from a public database (n = 11,265) and the Novitsky Lab (n=2,541). I generated time-scaled within-host phylogenies using BEAST, extracted indels by reconstructing ancestral sequences in Historian, and estimated variable loop indel rates …

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 Genetics Of The Genus Zamia (Zamiaceae, Cycadales), Michael Calonje

FIU Electronic Theses and Dissertations

The genus Zamia L. (Zamiaceae), consisting of 77 species, is the most species-rich and widely distributed cycad genus in the New World and is arguably the most morphologically and ecologically diverse genus in the Cycadales. We utilized a multilocus sequence dataset of 10 independent loci (9 single copy nuclear genes + 1 plastid) and extensive taxon sampling (over 90% of species) to infer phylogenetic relationships within Zamia. We infer a robust phylogenetic tree for the genus with a strong geographic delimitation of clades and find that four morphological characters typically used for diagnostic purposes in the genus exhibit a high …

Molecular And Morphological Variation Among Populations Of Pediomelum Tenuiflorum (Pursh) A.N. Egan (Fabaceae) In Nebraska, Usa, Chauncey L. Kellar Jr., Roxi Kellar

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

Individuals of Pediomelum tenuiflorum, “wild alfalfa”, from disjunct populations in Nebraska vary extensively in their overall gestalt. Those in the western and central part of the state have a very slender growth habit, with thin stems and few, small flowers; whereas, those in the southeast have a very robust growth habit with heavy-looking stems and many tightly clustered flowers. For nearly 200 years, taxonomists have alternated between splitting P. tenuiflorum into two species, with the many-flowered morphotype named P. floribundum, and lumping all the morphological variants into one species as they are now. In this study, we investigated …

Fusarium Euwallacea: A Serious Threat To The Native And Ornamental Trees And Shrubs In Southern California, Greg Tyler, Yixing Zheng, Michael Kulinich, Hagop Atamian

Student Scholar Symposium Abstracts and Posters

Fusarium Euwallacea is a fungus that has established symbiotic relationship with the beetle Euwallacea aff. fornicata. The beetle bores through the tree bark and into the sapwood making long tunnels inside the trees. The beetle carries the F. Euwallacea in a specialized structure on its body called mandibular mycangia and cultivates the fungus in the tunnels on which the beetle feeds to grow and reproduce. The growth of the fungus obstructs water and mineral transport in the plant xylem tissue, resulting in dieback, wilt and mortality of the host tree. Fungi are known to secrete proteins called effectors in …

Phylogeny Of The Australian Solanum Dioicum Group Using Seven Nuclear Genes: Testing Symon’S Fruit And Seed Dispersal Hypotheses., Christopher T. Martine, Ingrid E. Jordon-Thaden, Angela J. Mcdonnell, Jason T. Cantley, Daniel S. Hayes, Morgan D. Roche, Emma S. Frawley, Ian S. Gilman, David C. Tank

Faculty Journal Articles

The dioecious and andromonoecious Solanum taxa (the “S. dioicum group”) of the Australian Monsoon Tropics have been the subject of phylogenetic and taxonomic study for decades, yet much of their basic biology is still unknown. This is especially true for plant-animal interactions, including the influence of fruit form and calyx morphology on seed dispersal. We combine field/greenhouse observations and specimen-based study with phylogenetic analysis of seven nuclear regions obtained via a microfluidic PCR-based enrichment strategy and high-throughput sequencing, and present the first species-tree hypothesis for the S. dioicum group. Our results suggest that epizoochorous trample burr seed …

The Sucking Louse Fauna Of Mongolian Rodents: Host Associations, Molecular Phylogenetics And Description Of Two New Species, Chase N. Robinson

Honors College Theses

This study aimed to screen Mongolian rodents for sucking lice (Insecta: Phthiraptera: Anoplura) to better understand host-parasite associations for this understudied region. Nine species, including 3 previously undescribed, from 4 genera were identified. A molecular phylogeny based on 2 mitochondrial genes of collected louse specimens is included.

Comparative Mito-Genomic Analysis Of Different Species Of Genus Canis By Using Different Bioinformatics Tools, Ume Rumman, Ghulam Sarwar, Safia Janjua, Fida Muhammad Khan, Fakhra Nazir

Journal of Bioresource Management

In the current study, the mitochondrial genes sequence for COI, Cyt b and 16s rRNA of seven species found in different parts of the world were retrieved from NCBI Gene Bank while, PCR products of COI, Cyt b and 16s rRNA genes obtained from C. lupus and C.aureus present in Pakistan were sequenced and aligned for comparison. The phylogenetic analysis of mitochondrial COI, Cyt b and 16s rRNA genes showed almost the same results for the extant species of genus Canis. 16s rRNA revealed C. latrans, C. lycaon and C. simensis showed close phylogenetic relation with each other. …

Phylogenetic History Of The Amy Gene Cluster In Catarrhines, Christian M. Gagnon

Theses and Dissertations

This study phylogenetically analyzed 30 AMY-related genes from 11 primates. The results show the gradual expansion of the AMY gene family which could have allowed primates to adapt to various ecological landscapes and maximize energy intake from starch-rich foods in periods of food scarcity.

Multi-Locus Phylogenetic Inference Of The Howler Monkey (Alouatta) Radiation In South America., Esmeralda Ferreira

Dissertations and Theses

Abstract

Howler monkeys (Alouatta) are the most widely distributed New World primates, ranging from southern Mexico to northern Argentina. They occur in tropical rain forests, flooded and gallery forests, and deciduous and semi-deciduous environments. Despite their importance as seed dispersers, howlers have also been known to be ecological indicators. Available phylogenetic hypotheses for this genus have used chromosomal characters, morphological characteristics, and a limited number of molecular markers and specimens. In spite of these analyses, branching patterns among howler species lineages conflict between studies or remain unresolved. Using 14 unlinked non-coding intergenic nuclear regions under both a concatenated …

Phylogeny And Population Genetic Analyses Reveals Cryptic Speciation In The Bombus Fervidus Species Complex (Hymenoptera: Apidae), Jonathan B. Koch, Juanita Rodriguez, James P. Pitts, James P. Strange

Ecology Center Publications

Bumble bees (Bombus Latrielle) are significant pollinators of flowering plants due to their large body size, abundant setae, and generalist foraging strategies. However, shared setal coloration patterns among closely and distantly related bumble bee species makes identification notoriously difficult. The advent of molecular genetic techniques has increased our understanding of bumble bee evolution and taxonomy, and enables effective conservation policy and management. Individuals belonging to the North American Bombus fervidus species-complex (SC) are homogenous in body structure but exhibit significant body color phenotype variation across their geographic distribution. Given the uncertainty of the genealogical boundaries within the SC, some …

Identification And Characterization Of Nitrogen Fixing Bacteria Associated With Kudzu Root Nodules, Chasity Lawless, Michelle Zedonek, Debbie Curtis, Jonda Scharringhausen, Jared Bryant, Wendy A. Dustman, Alexandra M. Kurtz, Bekah Ward Dr.

Georgia Journal of Science

Pueraria montana, better known as kudzu, is an invasive species rapidly spreading throughout the southeastern United States. This plant can form root nodules which house nitrogen-fixing bacteria, allowing atmospheric nitrogen to be converted into biologically available forms of nitrogen for use by the plant host. Given the centrality of these bacteria to the spread of kudzu, isolates from nodules were characterized after collection from seven different locations across the metropolitan Atlanta area. Twenty-five isolates were grown on two different variants of nitrogen free media. Four different carbon sources were evaluated as well. Finally, growth under both aerobic and anaerobic …

Confirming World-Wide Distribution Of An Agriculturally Important Lacewing, Chrysoperla Zastrowi Sillemi, Using Songs, Morphology, Mitochondrial Gene Sequencing, And Phylogenetic Reconstruction, Zoe Mandese

Honors Scholar Theses

The Chrysoperla carnea-group of green lacewings is a cryptic species complex. Species within the group are morphologically similar, yet isolated from one another via reproductive mating song. Chrysoperla zastrowi, a species within the carnea-group, is currently described with a distribution ranging from South Africa to the Middle East and India. However, recent collections of carnea-group lacewings from Guatemala and California were preliminarily identified as Chrysoperla zastrowi based upon similarities in their vibrational courtship songs. This analysis aims to place six specimens, collected by collaborators in Guatemala, Armenia, Iran, and California, into a pre-existing phylogeny of the …

Population Structure, Demographic History, And Environmental Niche Of The Sand Fly Disease Vector Lutzomyia Shannoni (Dyar) (Diptera: Psychodidae) In The U.S., Mexico, And Colombia, Matthew E. Wolkoff

Biology Theses

Lutzomyia shannoni (Dyar, 1929) (Diptera: Psychodidae) is the only known sand fly vector of vesicular stomatitis virus, a putative leishmaniasis vector, and also boasts the widest distribution of any sand fly in the New World. Research on Lu. shannoni in Central and South America has revealed genetically divergent subpopulations; however, tentative analysis of Lu. shannoni in the U.S. has failed to detect any significant population structure, even between specimens collected from highly disparate localities.

The present study used four molecular markers to more closely investigate the population structure of Lu. shannoni in the U.S., and assess the species’ relationships with …