Doctor of Philosophy, Case Western Reserve University, 2025, Biomedical Engineering

The sex determining region Y-box (Sox) gene family is important for stem cells and early development in metazoans. Sox expression is associated with pluripotency, neuronal differentiation, developmental processes, and cancer. Platyhelminthes (flatworms) are flattened, bilaterally symmetrical invertebrates that lack body cavity. While there are many free-living species of flatworms, the most well-known flatworms are parasitic. Schistosome helminths infect over 200 million people across 78 countries and are responsible for nearly 300,000 deaths annually. We have characterized and a Sox-like gene SmSOXS1. SmSoxS1 is a developmentally regulated activator that localizes to the anterior and posterior ends of the schistosomula and binds to Sox-specific DNA elements. We also identified an additional six Sox genes in schistosomes, two Sox B, one SoxC, and three Sox genes that may establish a flatworm- specific class of Sox genes. To further explore this flatworm-specific group of Sox genes, we made a comparative analysis to identify Sox proteins in nine flatworm species, including S mansoni and S mediterenea. We identified 62 flatworm Sox proteins across the 9 species, 49 of them were unannotated. Using phylogenetic analysis, we found all of the flatworm species share a SoxD and SoxB homologs. In addition, we identified a clear flatworm-only group of sox proteins, observed in each flatworm species. Overall, we have identified novel Sox genes in schistosomes, and other flatworms. This thesis expands the potential functional roles for the Sox family and may provide interesting insights into early multicellular development of flatworms.

Committee: Emmitt Jolly (Advisor); Jean Burns (Committee Chair); Robert Ward (Committee Member); Brian McDermott (Committee Member); Nicole Crown (Committee Member) Subjects: Biology; Developmental Biology; Molecular Biology

Master of Science (MS), Bowling Green State University, 2024, Geology

Members of the Cretaceous ammonoid family Baculitidae are widely distributed and are known for being excellent index fossils. Despite the extensive work on baculitid biostratigraphy, little is known about the evolutionary relationships among baculitids. To address this knowledge gap, a Bayesian phylogenetic reconstruction of Late Cretaceous North American baculitid ammonoids was performed using the reversible jump Markov Chain Monte Carlo algorithm and fossilized birth-death process. Focusing on the genera Baculites, Sciponoceras, Trachybaculites, and Eubaculites, 25 characters from 43 baculitid species from the Eastern Pacific Coast, Western Interior Seaway, Gulf Coastal Plain, and Atlantic Coastal Plain were included in the dataset. Suture, shell shape, and ornamentation characters were partitioned to accommodate differences in evolutionary rates, and a timeline model was defined to allow origination and turnover rates to vary across ten defined time intervals. Model output demonstrated that suture characters had the highest evolutionary rates and ornamentation the lowest, with intermediate rates for shell shape characters. The Maximum Clade Credibility tree showed that Sciponoceras lineages are the most basal taxa and experienced budding cladogenesis. The genera Baculites, Eubaculites and Trachybaculites are not monophyletic, with species of the latter two genera derived from different Baculites species, including several instances of anagenesis. While baculitids of the Eastern Pacific are enigmatic compared to baculitids from other North American regions, the phylogenetic tree supports previous hypotheses of faunal interchange between the Eastern Pacific Coast and the Western Interior Seaway, despite the presence of Laramidia, the western iv North American landmass that separated the Pacific Ocean and Western Interior Seaway. Extinction, speciation, and sampling rates were also estimated. The highest speciation and extinction rate was during the Early Campania (open full item for complete abstract)

Committee: Margaret Yacobucci Ph.D. (Committee Chair); Jeffrey Snyder Ph.D. (Committee Member); Neil Landman Ph.D. (Committee Member) Subjects: Geology; Paleontology

Bachelor of Science (BS), Ohio University, 2024, Environmental and Plant Biology

Caryophyllaceae flowers have a wide range of morphological appearances, particularly in regards to their stamens and petaloids. In order to determine how these structures evolved, I reviewed the phylogenetic relationships, mature morphology, and developmental pathways of flowers in the family. I concluded that in addition to an antesepalous whorl of stamens, there was likely a whorl of some ancestral structure in the alternisepalous position. This structure may have been a petal, a stamen, or a transitionary staminode, but it diversified in various lineages into the numerous forms we see today.

Committee: John Schenk (Advisor) Subjects: Plant Biology

Doctor of Philosophy, The Ohio State University, 2023, Biostatistics

Combination tests are used to combine the results of individual hypothesis tests, often arising from independent studies, to draw reliable and generalizable conclusions about an underlying global null hypothesis. By pooling data from multiple studies, statistical combination tests can provide more accurate estimates of the effect size and increase statistical power beyond what may be possible with individual studies alone. Additionally, these tests can identify sources of heterogeneity or inconsistency across studies and provide insight into the factors that may influence the relationships between variables of interest. Other statistical approaches, such as meta-analysis, aim to combine results from multiple independent studies. However, unlike a combination test, meta-analysis requires several statistics, such as 95\% confidence intervals or odds ratios, which may not be available for all individual studies. Instead, we might only have access to the p-values from each study, and we may thus be unable to use meta-analysis. In this case, a combination test can be used to combine the individual p-values to test a global null hypothesis. In this dissertation, we show two different applications of combination tests in solving problems in phylogenetics and develop a novel combination test that performs well when only a small fraction of individual tests are expected to be significant. Methods based on the multi-species coalescence have been widely used in phylogenetic tree estimation using genome-scale DNA sequence data to understand the underlying evolutionary relationship between the sampled species. Evolutionary processes such as hybridization, which creates new species through interbreeding between two different species, necessitate inferring a species network instead of a species tree. A species tree is strictly bifurcating and thus fails to incorporate hybridization events which require an internal node of degree three. Hence, it is crucial to decide whether a t (open full item for complete abstract)

Committee: Laura Kubatko (Advisor); Sebastian Kurtek (Committee Member); Kellie Archer (Committee Member) Subjects: Biostatistics

Master of Science, The Ohio State University, 2022, Public Health

Understanding which regions of a genome are under selection is critical in order to enable effective responses to rapidly-evolving viruses. The need for such tools has been amplified by the recent COVID-19 pandemic. We apply two different methods of selection identification, a phylogenetic likelihood method and a simulation of the Wright-Fisher Diffusion model, to empirical data for SARS-CoV-2 obtained from the public GISAID repository. Phylogenetic Analysis by Maximum Likelihood (PAML) is an open source program developed by Ziheng Yang in 1997. We utilize PAML to identify sites within the COVID- 19 variant genomes which are experiencing positive selection. PAML uses a standard codon substitution model to compute likelihoods associated with various values of ω, a selection parameter which indicates positive selection if greater than 1. Results from PAML's M0, M3, and M8 models are compared. The M0 model estimates a single value of ω for an entire protein-coding region, while the M3 model estimates the K most likely values of ω within the protein-coding region of interest and associated probabilities, where K is user-specified. The M8 model estimates P (ω > 1) as a point mass and then generates a Beta distribution of probabilities associated with the remaining values of ω where P (ω < 1). We then conduct an alternative analysis using a continuous-time approximation to the Wright-Fisher model. The approximation is a stochastic differential equation (SDE) which describes the frequency of type A alleles over time and contains the selection parameter β. We simulate the model using the Euler Method, record the final allele frequency q, utilize q to estimate the likelihoods associated with various values of β, and then record the MLE of β for each SARS-CoV-2 variant. The results of the two analyses are compared, followed by a discussion of potential implications to the future state of the COVID-19 pandemic.

Committee: Laura Kubatko (Advisor); Asuman Turkmen (Committee Member); Kellie Archer (Committee Member) Subjects: Bioinformatics; Biostatistics; Genetics; Public Health; Statistics

Doctor of Philosophy, The Ohio State University, 2021, Horticulture and Crop Science

Plant breeders have used wild relatives as a source of genetic diversity for biotic and abiotic stress mitigation since the early 20th century. This natural allelic diversity is a vital resource for crop improvement. The focus of this dissertation was to use tomato as a model to compare two methods of accessing trait diversity from wild relatives: introgression breeding and grafting. The specific aims were to estimate the genetic and environmental contributions to trait delivery methods and assess their relative efficacy and limitations. An accession of the endemic Galapagos tomato, S. galapagense LA1141, provided allelic variation for the genetic dissection of purple fruit pigmentation and tolerance to water deficit stress. Accessions of S. pimpinellifolium and S. habrochaites were used as parents to develop interspecific hybrid rootstock for multi-year, multi-location field trials. The first objective was to determine the chemical and genetic basis of purple pigmentation. Accession LA1141 and a processing tomato, OH8245, were used to develop populations for the simultaneous characterization and introgression of traits. The breeding strategy employed repeated backcrossing (BC) followed by inbreeding (S). The LA1141 × OH8245 populations provided plant materials to identify genetic factors that underlie quantitative trait loci (QTL) while introducing these traits into a commercially viable genetic background. I genotyped the LA1141 × OH8245 BC2S3 generation with single nucleotide polymorphisms, created a linkage map, and conducted composite interval mapping. Anthocyanins were identified as causal pigments, and QTL analysis revealed genetic regions that explained as much as 35% of the variation in color. These analyses led to the identification of candidate genes. Subsequent sequence and phylogenetic analyses supported a conservation of mechanism leading to purple fruit, while identifying novel alleles at the Anthocyanin fruit, atroviolacium, and uniform ripening l (open full item for complete abstract)

Committee: David Fancis PhD (Advisor); Jessica Cooperstone PhD (Committee Member); Mathew Kleinhenz PhD (Committee Member); Chieri Kubota PhD (Committee Member); Christine Spunrger PhD (Committee Member) Subjects: Horticulture; Plant Biology; Plant Sciences

Doctor of Philosophy, The Ohio State University, 2021, Biostatistics

Phylogenetic trees are used to represent the evolutionary process that leads to ancestry-descent relationships among genetically differentiated populations. As an important characteristic of a phylogenetic tree, speciation times, or branch lengths, of the tree are of research interest in many problems. Because of affordable and rapid sequencing techniques that provide data about the branch lengths in the form of DNA sequences, it is possible and necessary to develop methods of inferring speciation times through modeling these DNA sequences. As an extension of trees, phylogenetic networks include hybridization/introgression events by adding horizontal edges to trees. Therefore, development of an efficient and accurate estimation method is also important for inferring parameters on a network. In this dissertation, we propose a novel speciation time estimator, called MAP-CL, for phylogenetic trees using DNA sequence data. This estimator differs from the existing methods in modeling the evolution of the DNA sequences directly, while achieving computational efficiency. We evaluate performance of this estimator under a variety of simulation settings and compare it with an existing, popular method through simulations as well as an empirical genome-scale dataset. We derive a closed-form expression for the composite likelihood of the speciation times under the JC69 model for the DNA substitution process and the multispecies coalescent model for the relationship between the speciation times and the evolutionary history of the individual genes. Then the MAP-CL estimator is derived by adding priors for the parameters and maximizing the posterior density. We prove that this estimator is statistically consistent and asymptotically normal, and use simulation studies to demonstrate these properties. Comparison with the Bayesian method BPP (Rannala and Yang, 2017; Yang and Rannala, 2014) shows that our estimator is comparatively accurate and efficient for large trees. Moreover (open full item for complete abstract)

Committee: Laura Kubatko (Committee Chair); Andrea Wolfe (Committee Member); Guy Brock (Committee Member) Subjects: Bioinformatics; Biostatistics; Evolution and Development

Doctor of Philosophy, The Ohio State University, 2021, Statistics

Inference of the evolutionary histories of species, commonly represented by a species tree, is complicated by the divergent evolutionary history of different parts of the genome. Different loci on the genome can have different histories from the underlying species tree (and each other) due to processes such as incomplete lineage sorting (ILS), gene duplication and loss, and horizontal gene transfer. The multispecies coalescent is a commonly used model for performing inference on species and gene trees in the presence of ILS. This thesis introduces Lily-T and Lily-Q, two new methods for species tree inference under the multispecies coalescent, and sets a framework for generalizing the Lily procedure to allow for differing mutation rates on different branches of the tree. Lily-T and Lily-Q are then compared to two frequently used methods, SVDQuartets and ASTRAL, using simulated and empirical data.

Committee: Laura Kubatko (Advisor); Radu Herbei (Committee Member); Matthew Pratola (Committee Member) Subjects: Biology; Evolution and Development; Statistics

Master of Science (MS), Ohio University, 2020, Geological Sciences

The evolution and biogeographic changes of three Ordovician brachiopod genera were examined using species-level phylogenetic analyses and phylogenetic biogeographic analyses in order to examine geological drivers of biogeographic evolution during the Great Ordovician Biodiversification Event (GOBE). Species-level phylogenetic hypotheses are reconstructed for Laurentian species of Hesperorthis Schuchert and Cooper 1931, Mimella Cooper, 1931, and Oepikina Salmon, 1942 using Bayesian inference. The reconstructed phylogenetic relationships were then used to investigate biogeographic patterns within the speciation of each lineage in order to evaluate how speciation occurred during the GOBE. Results indicate that alternating dispersal and vicariance events throughout the lineages of Hesperorthis, Mimella and Oepikina contributed to their increase in diversification during the Middle Ordovician which conforms to the BIME model of diversification. The oscillations of dispersal and vicariance events were related to fluctuating sea-level changes observed during the Middle to Late Ordovician.

Committee: Alycia Stigall Dr. (Advisor) Subjects: Geology; Paleontology

Master of Science, The Ohio State University, 2019, Evolution, Ecology and Organismal Biology

Sea anemones (order Actiniaria) are a diverse group of subclass Hexacorallia. Burrowing sea anemones have been historically grouped into the infraorder Athenaria (Carlgren 1899; Fautin 2013). Athenaria was revealed as polyphyletic (Daly et al. 2003, 2008, 2017; Rodriguez et al. 2014; Gusmao 2016). Haloclavidae is a family of burrowing sea anemones now grouped within the superfamily Actinioidea (Rafinesque 1815). This family includes 10 genera containing 30 species (Daly & Fautin 2019;2013 WORMS). Characters given for this family by Carlgren (1949) have a high range of variability, with numerous exceptions the expectations of the diagnosis (Rodriguez and Lopez-Gonzalez 2002). Previous phylogenetic analyses have shown that Haloclavidae is potentially a polyphyletic group (Rodriguez et al. 2012; Rodriguez et al. 2014; Daly et al. 2017), but resolution of relationships of the few representatives of Haloclavidae have been problematic. In Chapter 1, using mitochondrial and nuclear markers, I explore the systematics of Haloclavidae using three mitochondrial (COIII, 12S, 16S) and two nuclear markers (18S, 28S). I assess the monophyly of Haloclavidae by building a tree of this family within the superfamily Actinioidea. Additionally, I used parsimony-based character optimization to interpret the distribution of key traits in the superfamily. I find that Haloclavidae is not a monophyletic clade. Based on the results of my analyses and taxonomic considerations, I propose two new families, Peachiidae and Harenactidae, while also retaining some species in the family Haloclavidae. Family Haloclavidae will consist of 4 genera of anemones, some with acrospheres and some without. These genera are Anemonactis, Haloclava, Mesacmea, and Tenactis. Peachiidae includes four genera of anemones, all with a conchula and similar mesenterial arrangement (Antennapeachia Izumi, Yanagi and Fujita 2016, Metapeachia Panikkar Carlgren 1943, Peachia Gosse 1885, Synpeachia Yap, Fautin, Ra (open full item for complete abstract)

Committee: Meg Daly (Advisor); Rachelle Adams (Committee Member); Bryan Carstens (Committee Member) Subjects: Biology

Master of Science, University of Akron, 2019, Mathematics

The balanced minimum evolution (BME) polytope is a structure representative of a problem in biology, in particular in the study of phylogenetic trees. In this scope, the polytope is used to answer the question of how a set of species are related to one another. In this paper we explore generalized instances of the BME polytope for networks. For one of these generalized BME polytopes we focus on the discovery of new facets and their corresponding equations, while for the other we give the facets of the polytope and discuss the relationship that they have to another well known polytope outside of the field of biology. Furthermore, we also provide the dimension reducing equalities that were discovered which hold for every BME polytope and then prove their existence.

Committee: Stefan Forcey PhD (Advisor); Malena Espanol PhD (Committee Member); James Cossey PhD (Committee Member) Subjects: Mathematics

Master of Science (MS), Bowling Green State University, 2018, Biological Sciences

In an ongoing study of nuclear ribosomal DNA (rDNA) in fishes, unusually large (970 - 1418 bp) internal transcribed spacer (ITS1 and ITS2) regions were discovered in a wide diversity of members of the clade, Neoselachii (sharks, skates, and rays). This contrasts with the lengths for rDNA ITS regions in other eukaryotes, being larger by 30 to over 1000%. The additional segments of between 303 to 653 bp were due to insertions of single elements that have characteristics of group I introns, including conservation of structural and catalytic core regions. These spacer introns (spintrons) appear to be closest to the IC1 subgroup, although group I introns of any subtype have never been previously reported in the rRNA gene locus of any animal taxon. The aim for this study is to analyze the evolution of these spintrons. The current hypotheses are that these spintrons were inserted into an ancestor of Neoselachii and Batoidea, moved from one ITS region to the other, and then each evolved independently.

Committee: Scott Rogers Dr (Advisor); Paul Morris Dr (Committee Member); Vipaporn Phuntumart Dr (Committee Member) Subjects: Bioinformatics; Biology; Evolution and Development; Genetics; Wildlife Conservation

Master of Science (MS), Bowling Green State University, 2017, Applied Statistics (Math)

In this thesis, statistical methods are used to analyze the generation of species-level phylogenies. Two software packages, one phylogenetic and one statistical, are used to investigate the difference in phylogeny topology across three methods. Maximum likelihood estimation, neighbor-joining, and UPGMA methodologies are applied in this comparison to study the accuracy of each software package in correctly placing taxa with the true phylogeny. Four genes are used to compare with variable length sequences and genes amongst forty-seven squid species. In addition, missing data techniques are employed to assess the impact missing data has on phylogeny generation. Two software platforms were used to generate phylogenies for genes 16S rRNA, 18s rRNA, 28S rRNA, and the mitochondrial gene cytochrome c oxidase I (COI). The phylogenetic software platform MEGA was utilized as well as the statistical software platform, R; within R, the packages ape, phangorn, and seqinr were used in tree generation. Results show discrepancies between phylogenies generated across the four single-gene trees and multiple-gene trees; only phylogenies generated using missing data in the form of partial sequences grouped all families correctly. Results from this study highlight the struggle in determining the best software package to use for phylogenetic analyses. It was discovered that in general, MEGA generated a more accurate single-gene phylogeny from gene 18S rRNA while R generated a more accurate single-gene phylogeny from gene 28S rRNA. Results also showed that sequences with 50% missing characters could be accurately placed within generated phylogenies.

Committee: John Chen Dr. (Advisor); Junfeng Shang Dr. (Committee Member); Craig Zirbel Dr. (Committee Member) Subjects: Statistics

Master of Science (MS), Bowling Green State University, 2017, Geology

Both increased extinction and decreased origination, caused by rising oceanic anoxia and decreased provincialism, respectively, have been proposed as the cause of the Cenomanian Turonian (C/T) extinction event for ammonoids. Conflicting evidence exists for whether diversity actually dropped across the C/T. This study used the ammonoid superfamily Acanthoceratoidea as a proxy for ammonoids as a whole, particularly focusing on genera found in the Western Interior Seaway (WIS) of North America, including Texas. Ultimately, this study set out to determine 1) whether standing diversity decreased across the C/T boundary in the WIS, 2) whether decreased speciation or increased extinction in ammonoids led to a drop in diversity in the C/T extinction event, 3) how ecology of acanthoceratoid genera changed in relation to the C/T extinction event, and 4) whether these ecological changes indicate rising anoxia as the cause of the extinction. In answering these questions, three phylogenetic analyses were run that recovered the families Acanthoceratidae, Collignoniceratidae, and Vascoceratidae. Pseudotissotiidae was not recovered at all, while Coilopoceratidae was recovered but reclassified as a subfamily of Vascoceratidae. Seven genera were reclassified into new families and one genus into a new subfamily. After calibrating the trees with stratigraphy, I was able to determine that standing diversity dropped modestly across the C/T boundary and the Early/Middle Turonian boundary. I also found an increase in the percentage of genera becoming extinct in the Late Cenomanian, not a decrease in origination. Finally, I used Westermann morphospace to relate shell shape to ecology and mode of life. I found no decrease in morphospace occupation across the C/T boundary. More mobile modes of life expanded at this time. Morphospace occupation did drop across the Early/Middle Turonian boundary. All changes in morphospace occupation were driven by the family Vascoceratidae, (open full item for complete abstract)

Committee: Margaret Yacobucci (Advisor); Andrew Gregory (Committee Member); Keith Mann (Committee Member) Subjects: Geology; Paleontology

Master of Science, University of Akron, 2017, Applied Mathematics

Combinatorial methods have proved to be useful in generating relaxations of polytopes in various areas of mathematical programming. In this work, we propose a discrete-integer linear programming model for a recent version of the Phylogeny Estimation Problem (PEP), known as the Balanced Minimal Evolution Method (BME). We begin by examining an object known as the Balanced Minimal Evolution Polytope and several classes of geometric constraints that result in its relaxation. We use this information to develop the linear program and propose two Branch and Bound algorithms to solve the model. The second algorithm takes advantage of a heuristic known as a large neighborhood search. We provide experimental results for both algorithms, using perfect and noisy data, as well as suggestions for further improvement.

Committee: Stefan Forcey Dr. (Advisor); Malena Espanol Dr. (Committee Member); Patrick Wilber Dr. (Committee Member) Subjects: Applied Mathematics; Biology

Doctor of Philosophy, Case Western Reserve University, 2017, Biochemistry

Ribonucleotide reductase (RR) enables organisms to grow and reproduce by providing the deoxynucleotides necessary for DNA replication. Human RR can reduce any of the four nucleoside diphosphates at the 2' position, and binding of dNTP effectors (ATP/dATP, dGTP, dTTP) modulates substrate specificity at an allosteric site near the active site. This binding is known to change the conformation of a short loop (loop 2) that bridges the two sites. Although the relationship between effector binding and enzymatic specificity is well-established, the specific interactions through which RR recognizes the effector and changes the conformation of loop 2 remain untested. The precise interconnecting roles of the individual amino acid residues in loop 2 are also unclear. Here, we systematically interrogate the contribution of each effector functional group using a panel of dNTP analogues and multiple substrate kinetic assays, and confirm a key prediction from crystal structures by showing that interactions with amino acid residue D287 in loop 2 are essential for perturbing its conformational space. In addition, we examine natural variation in loop 2 among eukaryotes as an alternative to more traditional alanine mutagenesis. We find that amino acid sequence space among eukaryotes is dominated by two major types of loop 2, and that they differ by just two substitutions, and these substitutions are highly nonconservative with respect to structure (N291G and P294K). Simultaneously introducing both mutations into human RR partially rescues the effects of the single mutations. This work sheds light on a key molecular mechanism by which organisms generate balanced dNTP pools for timely and accurate DNA replication and repair.

Committee: Michael Harris Ph.D. (Advisor) Subjects: Biochemistry

Doctor of Philosophy, The Ohio State University, 2016, Geological Sciences

Phylogenetic paleobiology is an interdisciplinary research program at the nexus of paleontology, systematics, and evolutionary biology. Specifically, phylogenetic paleobiology integrates the deep-time data, techniques, and geologic perspectives of paleontology with phylogeny-based statistical and computational approaches in macroevolutionary biology. Chapters contained within this dissertation revolve around two primary themes: (1) understanding patterns of biodiversity change over geologic time, and (2) assembling a clearer picture of the phylogeny, evolution, and geologic history of marine invertebrates, especially the Crinoidea (Echinodermata). Under the umbrella of phylogenetic paleobiology, the primary objective of this dissertation is to help bridge the disciplinary gap between specimen-based paleontology and statistical approaches in phylogenetic comparative methods. The chapters herein use advanced statistical phylogenetic methods, such as Bayesian “tip-dating” approaches, to infer phylogenetic trees of fossil species, quantify rates of phenotypic evolution, and document patterns of morphospace occupation among fossil members of the Crinoidea (Echinodermata). In addition to these broader studies, a major taxonomic revision of fossil and extant Crinoidea (Echinodermata) is proposed herein, as well as taxonomic description of a new genus of fossil crinoid from the Ordovician (Katian) of Ontario.

Committee: William Ausich (Advisor); Matthew Saltzman (Committee Member); Lawrence Krissek (Committee Member); John Freudenstein (Committee Member) Subjects: Evolution and Development; Geology; Paleontology

Master of Science (MS), Ohio University, 2017, Biological Sciences (Arts and Sciences)

Phylogenetic niche conservatism (PNC) is the retention of ancestral ecological characteristics among related species, more so than would be expected by a simple Brownian motion process. PNC may be important in explaining biodiversity gradients, species' ranges, and species formation, but an ecological cause for PNC has been challenging to identify. One hypothesis is that PNC occurs when ecological opportunity (exposure to new, accessible niche space) is lacking. Ecological opportunity may be unavailable when habitats are ecologically saturated, but conversely, the availability of depauperate environments may provide opportunity. Because eastern Plethodon salamanders are characterized by strong PNC, studying a species within Plethodon characterized by niche lability may elucidate why PNC occurs. I investigated the biogeography of the Eastern Red-backed Salamander (Plethodon cinereus) and tested the hypothesis that the climatic niche of P. cinereus diverged when glacial retreat made competitor-free habitats available. I addressed this hypothesis by sampling 202 individuals from 107 populations throughout the range of P. cinereus, and I analyzed molecular sequences for three mitochondrial and three nuclear loci, totaling 4,686 base pairs. A time-calibrated phylogeny was inferred with the Bayesian phylogenetic program BEAST. Among intraspecific clades, I tested for climatic niche divergence and compared rates of evolution using climatic data. I found that three different clades invaded areas north of the last glacial maximum (LGM), with one clade occupying most of the range beyond the LGM. Niche models and rates of climatic niche evolution were compared between clades. Consistent with the ecological opportunity hypothesis, I found that the rate of climatic niche evolution was significantly greater for populations that colonized areas north of the LGM. This study provides an ecological explanation for PNC and its converse, niche lability, by examining the climatic niche (open full item for complete abstract)

Committee: Shawn Kuchta (Advisor); Morris Molly (Committee Member); White Matthew (Committee Member) Subjects: Biology; Ecology

Doctor of Philosophy, The Ohio State University, 2016, Evolution, Ecology and Organismal Biology

Penstemon Mitchell (Plantaginaceae) is the largest plant genus endemic to North America with approximately 280 species. Most species are only relatively recently diverged from one another, which has left questions about taxonomy and systematics in Penstemon unanswered. This dissertation considered one section in the genus, Ericopsis Keck, a group of 15 species from the Intermountain Region in western USA. Evolutionary and ecological frameworks were used to investigate phylogenetic relationships, population demographic history, polyploidy, and niche divergence. Chapter 1 presents the results of a phylogenetic study of section Ericopsis. Using a total of 39 nuclear and chloroplast loci obtained from high-throughput targeted sequencing and Sanger sequencing the exact membership of section Ericopsis was able to be determined. This included two taxa not currently classified in section Ericopsis, P. pinifolius and P. dolius var. dolius. It was also determined that three current Ericopsis species, P. acaulis, P. yampaensis, and P. laricifolius, group in a clade with species from section Cristati with high support. Within the Ericopsis clade, however, nodal support for relationships among species was low, so strong conclusions about exact relationships are difficult to ascertain. There was support for a clade comprising the species of subsection Linarioides, as well as groups consisting of the varieties of P. caespitosus and P. crandallii. It is likely that incomplete lineage sorting and hybridization are causing gene tree incongruence in these analyses, which may be alleviated by adding additional sequence data from informative loci. Chapter 1 also provides the context for questions asked in subsequent chapters of the dissertation. Chapters 2 and 3 use a population genetics framework to study evolutionary dynamics in two widespread species from section Ericopsis. In chapter 2 the variable P. linarioides Gray is considered. This population genetics study i (open full item for complete abstract)

Committee: Andrea Wolfe (Advisor); John Freudenstein (Committee Member); Laura Kubatko (Committee Member); Stephen Matthews (Committee Member) Subjects: Biology; Plant Biology

Doctor of Philosophy, The Ohio State University, 2016, Evolution, Ecology and Organismal Biology

The Nematalycidae are among the most bizarre looking arthropods; their extreme body elongation is an especially unusual modification within the Arachnida. However, there have been few attempts to study their morphology in detail. This is partly because there are few available specimens – they live in mineral regolith, which is sampled relatively rarely. But this is also due to their extremely small size and soft integument. The former makes them problematical for examination under a light microscope; the latter renders them inappropriate for conventional scanning electron microscopy. This dissertation is a body of work that attempts to address this knowledge gap via low-temperature scanning electron microscopy (LT-SEM). Chapter 2 is a description of a new genus and species. Chapter 3 addresses how the two main different modes of locomotion, one of which is a novel discovery, correspond with modifications of the integument. Chapters 4 and 5 are concerned with hypotheses on adaptations of the gnathosomas (mouthparts) of three different genera. Chapter 4 includes a hypothesis on a novel form of microbivory, which could explain some of the gnathosomal features of Osperalycus and Gordialycus. Chapter 5 addresses the evolutionary implications of the mouthparts of Cunliffea, which has a rudimentary sheath for chelate (`biting') chelicerae. This structure may help to explain how one of the unusual modifications of the Eriophyoidea, a stylet sheath, originated. Chapter 6 concerns a phylogenetic analysis of morphological characters. The principal finding is that the Eriophyoidea, a diverse group of plant parasites, are more closely related to the Nematalycidae than any other lineage, and they may even be derived from within the Nematalycidae. Therefore, the unusual, vermiform bodies of these two taxa are shared because of their relatively recent common ancestry, and not because of evolutionary convergence. In the final chapter, the conclusion, I suggest that the Nematalyci (open full item for complete abstract)

Committee: Hans Klompen (Advisor); Norman Johnson (Committee Member); Daly Meg (Committee Member) Subjects: Animal Sciences; Entomology; Morphology