Evolution Commons^™

The Hitchhiker's Guide To The Host: Fleas And The History Of Pikas In North America, Josh Pletcher

All NMU Master's Theses

Parasite phylogenetics can offer windows into the cryptic evolutionary history of hosts, often highlighting events that are not recorded by the phylogenetics of the host. Pikas (small lagomorphs) host a diverse parasite community comprising endoparasites (e.g., coccidians, nematodes, and cestodes) and ectoparasites (e.g., fleas and mites). Phylogenetic analysis of pika endoparasites has revealed pikas evolved in Asia and colonized North America in two waves, and that contact between these two pika lineages allowed parasites to be transferred from one lineage to another and to survive the extinction of their original host. To uncover these cryptic histories, understanding the biogeography of …

Phylogenetic Comparative Vocal Evolution, Casper W. Buchanan

Master's Theses

Vocal learning is a trait unique to humans, bats, cetaceans, primates, and birds (Jarvis & Nottebohm, 1997; McComb & Semple, 2005; Wilbrecht & Nottebohm, 2003). Although there has been extensive research on vocal learning in songbirds, parrots are an even closer proxy to human learning, as they are social, intelligent, and lifelong learners, with some having repertoires of over 300 sounds (Benedict et al., 2022; Péron et al., 2011; Thomsen et al., 2019; Toft & Wright, 2015). Elevated vocal learning can be attributed to the need for parrots to have strong communication skills through the sharing of information over foraging, …

Systematics, Biogeography, And Comparative Morphology Of Emerald And Tigertail Dragonflies (Anisoptera: Synthemistidae & Corduliidae), Aaron M. Goodman

Dissertations, Theses, and Capstone Projects

Dragonflies and damselflies (Odonata Fabricius, 1793) are among the most widely recognized and charismatic insect groups, whose significance have permeated throughout artwork, culture, and religion. They are highly mobile predators, currently consisting of ~ 6,500 species, and possessing some of the complex visual color systems, visual acuity, and flight patterns on Earth. Odonata are the among the earliest flying insects, with proto-odonates (Griffinflies) dating back to the Carboniferous (~360mya), with crown-odonata fossils stretching back to the Triassic (~250mya). Overall, dragonflies and damselflies are considered models of ecological and evolutionary research due to their long evolutionary history, range of habitats, and …

Systematics Of African River Frogs (Anura: Pyxicephalidae: Amietia) In Central Africa, With The Description Of Two New Species, Jesus Manuel Reyes

Open Access Theses & Dissertations

Amietia is a pyxicephalid anuran genus that is prevalent throughout central, southern, and eastern portions of sub-Saharan Africa. Recent phylogenetic studies have been in conflict regarding the validity and composition of several Amietia species in the Albertine Rift region. The goals of this study are to: (1) generate an updated molecular phylogeny for Central African Amietia with new sampling; (2) clarify the relationship between the previously unsampled taxa A. amieti and A. chapini; (3) clarify the status of A. desaegeri; and (4) confirm the taxonomic status of potentially new species. Maximum likelihood and Bayesian inference methods were used to generate …

A Phylogeographic Study Of The Kentucky Endemic Cave Beetle Neaphaenops Tellkampfii Erichson (1844), Mahamad Miya

Masters Theses & Specialist Projects

Cave beetles are an excellent group to study evolutionary history and speciation by isolation within cave habitats. However, they are underrepresented in such studies, particularly in North America, one of the hotspots of cave biodiversity where beetles account for a significant proportion. The present research addresses this issue by focusing on the Kentucky endemic cave beetle, Neaphaenops tellkampfii, a species hypothesized to comprise four subspecies. Based on allozyme data, previous studies have noted high genetic variation within and high similarity among local populations of this beetle, suggesting complex evolutionary dynamics. In this regard, this study aims to elucidate the evolutionary …

Evolution And Adaptation To Temperature In Thermotogota, Anne Amelia Farrell

Dartmouth College Ph.D Dissertations

Life thrives across incredibly diverse environmental conditions, yet most organisms are restricted to growing within a narrow range around their optimum growth temperature (OGT). The evolutionary events leading to changes in OGT are poorly understood, and it is uncertain if specific genes are required to thrive at a particular temperature. The bacterial phylum Thermotogota is an excellent model for the evolution of OGT. It comprises mesophilic, thermophilic, and hyperthermophilic members that collectively grow between 20°C and 90°C.

In this work, I analyze the history of OGT in the Thermotogota phylum and show how horizontal gene transfer contributes to the evolution …

Unraveling The Paradox Of The 'Great Speciators': Evolutionary Dynamics Of A Geographic Radiation Of Island Kingfishers (Todiramphus), Jenna Merle Mccullough

Biology ETDs

The paradox of the ‘Great Speciators’ describes a biogeographic pattern in which geographically widespread lineages have strong overwater dispersal capabilities, yet exhibit genetic and phenotypic divergence between islands, suggesting limited dispersal and cessation of gene flow. In my dissertation, I leveraged whole genomes and two comprehensive trait datasets of dispersal ability and plumage coloration of all described diversity within Todiramphus kingfishers, a rapid radiation of largely island endemic ‘Great Speciators.’ Chapter 1 reveals that whole genome datasets do not outright solve the evolutionary relationships of this clade and that widespread incomplete lineage sorting (ILS) and gene flow are sources of …

Bioinformatic Comparison And Salinity Tolerance Of Various Cyanobacterial Strains, Lucie Rowe

Honors Theses

Cyanobacteria are an abundant and diverse group of photosynthetic prokaryotes with a long evolutionary history, which presents challenges for comprehensive taxonomic classification. Phylogenies were traditionally constructed based on the highly conserved 16S rRNA gene, but research has increasingly relied upon whole genome sequencing to elucidate evolutionary relationships, despite increased cost and time. In this thesis, publicly available genome sequences of various cyanobacterial strains were utilized to determine if the whole rRNA region, which includes the 16S, 23S, and 5S genes as well as the spacer regions between, could provide accurate, yet cost/time efficient representations of their evolutionary relationships. From phylogenetic …

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 …

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 …

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 …

Historical Dna Solves An Evolutionary Mystery And Explains The Origin Of A Novel Phenotype In The New World Quails, Jessie Frances Salter

LSU Doctoral Dissertations

Observations of phenotypic diversity among closely-related organisms, especially those preserved as museum specimens, have driven the fields of systematics, taxonomy, and evolutionary biology for hundreds of years. In this dissertation, I used genomic data from modern and historical specimens to investigate the evolutionary processes that have generated phenotypic and genetic diversity in a highly polytypic group of birds, the New World quails (Odontophoridae), with a focus on the most phenotypically diverse member of this family: Northern Bobwhites (Colinus virginianus). To facilitate this work, I began by generating a highly contiguous reference genome assembly for Northern Bobwhites, which is …

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 …

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 …

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 …

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 …

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 …

Systematics Of Carex Section Laxiflorae (Cyperaceae), Jenna Dorey

Dissertations, Theses, and Capstone Projects

Carex, with more than 2100 species, is the most species-rich genus of flowering plants in temperate regions of the world. Members of the family Cyperaceae are colloquially known as sedges, and members of the genus Carex are called “true sedges.” Carex occur on every continent except for Antarctica, they thrive in a panoply of habitats, and are ecologically important as a forage source for wildlife, carbon sequestration, prevention of soil erosion, and providing habitat for fresh water invertebrates. Despite their importance many sedges are still poorly known, such as the woodland sedges in Carex section Laxiflorae, which is …

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 …

Phylogeny And Evolution Of Swallows (Hirundinidae) With A Transcriptomic Perspective On Seasonal Migration, Clare Elisabeth Brown

LSU Doctoral Dissertations

Evolutionary biology seeks to understand the forces that have generated and shaped patterns of diversity. In this dissertation, I investigated phylogenetic relationships and the evolution of three traits—migration, nest-type, and geographic distribution—in the swallow family (Hirundinidae), a globally distributed group of about 85 species of aerial insectivorous birds. I first applied a dataset of several thousand ultraconserved element (UCE) loci to reconstructing the phylogeny of the New World genus Tachycineta. Three methods of phylogenetic inference produced topologically discordant trees, but post-inference analyses provided evidence that the tree produced by maximum likelihood analysis of a concatenated data matrix is the most …

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 …

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 …

Understanding Patterns Of Diversity And Evolution In Mainland Anolis Lizards, Levi Nathaniel Gray

Biology ETDs

Patterns of organismal diversity and evolution are often difficult to interpret with a high level of confidence. The number of mechanisms and processes that contribute to shaping patterns of diversity is extensive and is reflected in the many methods researchers have used to infer causation. Taxonomic groups that are well-studied can offer more precise interpretation of pattern and process due to the considerable amount of research addressing ecology, natural history, and behavior of the organisms.

In this dissertation, I explore patterns of phylogenetic and phenotypic variation in Anolis lizards (anoles) by testing hypotheses that could have led to the observed …

Using Molecular Markers To Trace The Population History Of Volant Organisms At Differing Temporal Scales, Noah A. Burg

Dissertations, Theses, and Capstone Projects

Using molecular markers to test phylogenetic and phylogeographic hypotheses is critical for tracking the population origin of invasive, introduced species (Chapter 2, Chapter 4) and to identify the systematic relationships of disparate lineages at both shallow and deep evolutionary time scales (Chapters 3, Chapter 4). In this thesis, Sanger Sequencing was used to generate datasets based on fresh and preserved tissue from specimens collected in the field, as well as museum tissue vouchers granted from various institutions in the US and Europe. In combining these source materials, data were generated for three focal studies: 1) In the first research section …

A Contribution Toward A Global Monograph Of Gyroporus: Taxonomy, Phylogeny, Biogeography, Naveed Davoodian

Dissertations, Theses, and Capstone Projects

Gyroporus (Sclerodermatineae, Boletales, Agaricomycetes, Basidiomycota, Fungi) is a genus of ectomycorrhizal mushroom-forming fungi distributed throughout the world in suitable habitats. Previous attempts to untangle the diversity of this genus proved difficult due to the presence of semi-cryptic species and equivocal results from phylogenetic analysis of ribosomal RNA markers. To overcome these obstacles, a combined taxonomic and phylogenetic (emphasizing protein-coding genes) approach is used here to delimit species and elucidate geographic and evolutionary patterns of Gyroporus. Careful study of relevant literature and herbarium specimens was augmented by field work in North America, Australia, and East Asia for observation and collection …

Comparative Phylogeography, Taxonomy, And Neuroanatomy Of Montane Chameleons In The Albertine Rift, Central Africa, Daniel Hughes

Open Access Theses & Dissertations

How do traits vary across the tree of life? Our ability to address this question is diminished if: A taxonomic group has a poorly sampled phylogeny, a species goes extinct before their systematic position is resolved, or a trait is inadequately characterized for detailed studies. In the current era of mass extinction, it is imperative to not only accelerate species discovery through traditional studies in taxonomy and expeditionary research, but also to increase rescue efforts for all types of data before poorly understood species and potentially undescribed traits are lost. Here, an integrative taxonomic approach was used and novel methods …